University of Washington - SAFS - Roberts Lab

qPCR Analysis - C.gigas Lifestages Carryover

2024
Crassostrea gigas
Pacific oyster
qPCR
project-gigas-carryover
lifestage_carryover
This notebook performs pair-wise comparisons of qPCR gene expression, normalized to GAPDH expression. It calculates delta Cq, delta delta Cq, and fold changes in expression.…
Dec 20, 2024
Sam White

qPCR - C.gigas Lifestage Carryover VIPERIN

2024
Crassostrea gigas
Pacific oyster
SsoFast
CFX Connect
CFX96
project-gigas-carryover
VIPERIN
Continuing work with project-gigas-carryover lifestage_carryover (GitHub repo) after creating cDNA on 20241024 (Notebook entry), it was finally time to run the qPCRs. Three…
Dec 12, 2024
Sam White

qPCRs - C.gigas Lifestage Carryover citrate synthase DNMT1 HSP70 and HSP90

2024
Crassostrea gigas
Pacific oyster
SsoFast
CFX Connect
CFX96
project-gigas-carryover
citrate synthase
DNMT1
HSP70
HSP90
Continuing work with project-gigas-carryover lifestage_carryover (GitHub repo) after creating cDNA on 20241024, it was finally time to run the qPCRs. Three primer sets were…
Dec 11, 2024
Sam White

Screenshot of MD5 checksum verifications.

Data Received - Coral E5 sRNA-seq Time Series Azenta Project 30-1069297013

2024
coral
E5
sRNA-seq
timeseries_molecular
Data Received
30-1069297013
We received sRNA-seq data from Azenta project 30-1069297013. is in. All files were downloaded and MD5 checksums were verified. Raw FastQ files are available here:
Dec 10, 2024
Sam White
 

miRNA Identification - R.phillipinarum sRNA-seq Using ShortStack and miRBase Mature miRNAs

2024
Ruditapes phillipinarum
Manila clam
sRNA-seq
miRNA
project-clam-oa
ShortStack
miRBase
This notebook is part of project-clam-oa (GitHub repo).
Dec 10, 2024
Sam White

qPCRs - C.gigas Lifestage Carryover GAPDH ATP_synthase and cGAS

2024
Crassostrea gigas
Pacific oyster
GAPDH
ATP synthase
cGAS
SsoFast
CFX Connect
CFX96
project-gigas-carryover
Continuing work with project-gigas-carryover lifestage_carryover (GitHub repo) after creating cDNA on 20241024, it was finally time to run the qPCRs.
Dec 10, 2024
Sam White

Trimming and Merging - R.philippinarum sRNA-seq Data Using fastp FastQC and MultiQC

2024
Ruditapes philippinarum
Manila clam
project-clam-oa
sRNA-seq
This notebook is part of project-clam-oa (GitHub repo).
Dec 6, 2024
Sam White

FastQ Concatentation and QC - R.philippinarum sRNA-seq Data Using FastQC and MultiQC

2024
Manila clam
Ruditapes philippinarum
30-1035633055
30-1035633055-TS01
project-clam-oa
FastQC
MultiQC
This notebook is part of project-clam-oa (GitHub repo).
Dec 5, 2024
Sam White

Methylation Extraction - C.virginica CEASMALLR WGBS Using Bismark

2024
Crassostrea virginica
Eastern oyster
ceasmallr
wgbs
BS-seq
Bismark
methylation extraction
This notebook is part of the ceasmallr (GitHub repo) project, comparing DNA methylation in Crassostrea virginica (Eastern oyster) larvae and zygotes, via whole-genome…
Nov 26, 2024
Sam White

Deduplication - C.virginica CEASMALLR WGBS Using Bismark

2024
Crassostrea virginica
Eastern oyster
ceasmallr
Bismark
WGBS
BS-seq
deduplication
This notebook is part of the ceasmallr (GitHub repo) project, comparing DNA methylation in Crassostrea virginica (Eastern oyster) larvae and zygotes, via whole-genome…
Nov 25, 2024
Sam White

Computer Management - Replace Failed Hard Drive on Gannet

2024
Gannet
HDD
Computer Management
Gannet was inaccessible, so went into lab to investigate. When I arrived, Gannet appeared to be powered on and the “Status” light was green, but none of the drive light…
Nov 18, 2024
Sam White
 

Alignment - C.virginica CEASMALLR WGBS Using Bismark on Klone Array

2024
trimming
Crassostrea virginica
Eastern oyster
ceasmallr
WGBS
BS-seq
Klone
Bismark
This notebook is part of the ceasmallr (GitHub repo) project, comparing DNA methylation in Crassostrea virginica (Eastern oyster) larvae and zygotes, via whole-genome…
Nov 18, 2024
Sam White

FastQC adaptor sequences plot showing excessive polyG sequences in CF03-CM03-Zygote_R1.

Trimming and QC - C.virginica CEASMALLR FastQs Using fastp BBTools and FastQC-MultiQC

2024
trimming
FastQC
fastp
BBTools
MultiQC
Crassostrea virginica
WGBS
BS-seq
bisulfite
Eastern oyster
ceasmallr
This notebook is part of the ceasmallr (GitHub repo) project, comparing DNA methylation in Crassostrea virginica (Eastern oyster) larvae and zygotes, via whole-genome…
Nov 15, 2024
Sam White

Taxonomic Classification - Trinity Assembly of Unmapped P.helianthoides RNA-seq Using DIAMOND BLASTx and MEGAN6 on Mox

2024
DIAMOND
BLASTx
MEGAN6
Pycnopodia helianthoides
sunflower sea star
Mox
In preparation for a grant proposal involving sea star wasting disease, due in about two weeks, Steven asked that I perform taxonomic classification on a Trinity assembly of…
Nov 8, 2024
Sam White

FastQ QC - M.trossulus WGBS from Psomagen Using FastQC and MultiQC

2024
Mytilus trossulus
WGBS
Psomagen
FastQC
MultiQC
mussel
project-mytilus-methylation
This is part of Chris’ project-mytilus-methylation(GitHub repo). Data was received from Psomagen on 20241101 (Notebook entry). I performed the initial QC using FastQC and Mul…
Nov 7, 2024
Sam White

Trimming and QC - M.trossulus WGBS Using fastp and FastQC-MultiQC

2024
Mytilus trossulus
WGBS
fastp
FastQC
MultiQC
bay mussel
project-mytilus-methylation
trimming
This is part of Chris’ project-mytilus-methylation(GitHub repo). Data was received from Psomagen on 20241101 (Notebook entry). I performed the initial QC using FastQC and Mul…
Nov 7, 2024
Sam White
 

Data Wrangling - GO to GOslims for Graces Dermasterias imbricata Project from Trinity Assembly Genes

2024
Dermasterias imbricata
GO
GOslim
gene ontology
Trinity
Leather star
This notebook consists of a markdown rendering of 01-GO-to-GOslim.Rmd (commit: 04a796d).
Nov 6, 2024
Sam White
 

Data Wrangling - GO to GOslims for Graces Pycnopodia helianthoides Project from Trinity Assembly Genes

2024
GO
gene ontology
GOslim
Pycnopodia helianthoides
Trinity
Sunflower sea star
This notebook consists of a markdown rendering of 01-GO-to-GOslim.Rmd (commit: 3b642b4).
Nov 6, 2024
Sam White

Sequencing Read Taxonomic Classification - Unmapped P.helanthoides RNA-seq Using DIAMOND-BLASTx and MEGAN6 on Mox

2024
MEGAN6
RNAseq
DIAMOND
BLASTx
Pycnopodia helianthoides
sunflower sea star
Mox
In preparation for a grant proposal involving sea star wasting disease, due in about two weeks, Steven asked that I perform taxonomic classification on unmapped…
Nov 5, 2024
Sam White

Data Received - Manila clam Supplemental sRNA-seq Data from Azenta

2024
sRNA-seq
Manila clam
Ruditapes philippinarum
30-1035633055
30-1035633055-TS01
Data Received
Received supplemental sRNA-seq data for Azenta Project 30-1035633055, since the previous data sent (Notebook) didn’t amount to the minimum expected read count for a number…
Nov 1, 2024
Sam White

Screenshot showing successful MD5 checksum verifications.

Data Received - Mytilus trossulus WGBS Data from Psomagen

2024
Mytilus trossulus
bay mussel
WGBS
Psomagen
AN00021156
BS-seq
bisulfite sequencing
Data Received
Received WGBS data for Chris’ Psomagen Project AN00021156.
Nov 1, 2024
Sam White
 

Daily Bits - November 2024

2024
Daily Bits
  • Installed RepeatMasker on Raven (GitHub Issue). Installed with dfam38_full.0.h5 repeats partition/database. Deatils on the database here…
Nov 1, 2024
Sam White
 

Data Wrangling - Get GOslims from GO IDs for Graces Pycnopodia helianthoides Project

2024
Pycnopodia helianthoides
sunflower sea star
gene ontology
GO
GOslim
data wrangling
This notebook consists of a markdown rendering of 01-GO-to-GOslim.Rmd (commit: 351b2ad).
Oct 30, 2024
Sam White

DNA Isolation Quantification and Gel - Lake Trout Liver Samples

2024
DNA isolation
Qubit
DNA quantification
agarose gel
lake trout
Salvelinus namaycush
liver
Steven asked that I isolate gDNA from a subset of lake trout (S.namaycush) liver samples (GitHub Issue).
Oct 25, 2024
Sam White

Reverse Transcription - C.gigas Lifestage Carryover RNA

2024
reverse transcription
cDNA
GoScript
Crassostrea gigas
Pacific oyster
RNA
project-gigas-carryover
lifestage_carryover
Continuing with Ariana’s request to extract RNA and run qPCRs (GitHub Issue) for the lifestage_carryover project (GitHub repo), I performed reverse transcription on RNA I…
Oct 24, 2024
Sam White

New external drive isn't listed (i.e. isn't automounted) after being plugged in.

Computer Management - Configure 16TB OWC ThunderBlade X8 External HDD on Raven

2024
Computer Management
HDD
We recently purchased a 16TB OWC ThunderBlade X8 as additional storage for Raven (Ubuntu 18.04LTS), primarily to be used for Shelly and Emma’s project. Although I thought…
Oct 21, 2024
Sam White

PCR cycling parameters.

PCR - Lake Trout C1q Primers with Bisulfite-treated gDNA

2024
C1q
Lake trout
Salvelinus namaycush
PCR
bisulfite
gDNA
liver
gel
The original _Salvelinus namaycush C1q bisulfite PCR on 20240911 (Notebook) using bisulfite primers designed on 20240729 (Notebook) failed to produce any amplification. In…
Oct 9, 2024
Sam White
 

RNA-seq Alignment - A.pulchra RNA-seq Alignments Using HISAT2 and StringTie for Azenta Project 30-1047560508

2024
30-1047560508
RNA-seq
E5
timeseries_molecular
HISAT2
StringTie
alignment
Acropora pulchra
coral
This notebook entry is knitted from urol-e5/timeseries_molecular/D-Apul/code/02.20-D-Apul-RNAseq-alignment-HiSat2.Rmd (GitHub), commit 0f801c0.
Oct 8, 2024
Sam White
 

Data Wrangling - Generate GTF from A.pulchra Genome GFF Using gffread

2024
coral
Acropora pulchra
genome
GFF
GTF
gffread
E5
timeseries_molecular
This notebook entry is knitted from urol-e5/timeseries_molecular/D-Apul/code/02.00-D-Apul-RNAseq-gff-to-gtf.Rmd (GitHub), commit cf654b9.
Oct 8, 2024
Sam White
 

Genome Indexing - A.pulchra Genome Using HISAT2

2024
coral
Acropora pulchra
HISAT2
E5
timeseries_molecular
This notebook entry is knitted from urol-e5/timeseries_molecular/D-Apul/code/02.10-D-Apul-RNAseq-genome-index-HiSat2.Rmd (GitHub), commit da11371.
Oct 8, 2024
Sam White
 

FastQC Trimming and QC - A.pulchra RNA-seq from Azenta Project 30-1047560508 Using fastp

2024
RNA-seq
30-1047560508
Azenta
coral
Acropora pulchra
fastp
FastQC
MultiQC
trimming
E5
timeseries_molecular
This Rmd file trims A.pulchra RNA-seq files using fastp (Chen 2023), followed by quality checks with FastQC and MultiQC (Ewels et al. 2016).
Oct 5, 2024
Sam White
 

FastQ QC - A.pulchra RNA-seq from Azenta Project 30-1047560508

2024
RNA-seq
30-1047560508
Azenta
coral
Acropora pulchra
FastQC
MultiQC
timeseries_molecular
E5
This notebook entry is knitted from urol-e5/timeseries_molecular/D-Apul/code/00.00-D-Apul-RNAseq-reads-FastQC-MultiQC.Rmd (GitHub), commit b7a80be.
Oct 4, 2024
Sam White
 

Daily Bits - October 2024

2024
Daily Bits
Downloaded updated RNA-seq data, from Azenta, which was previously incomplete.
Oct 1, 2024
Sam White

MD5 checksum verification.

Data Received - R.philippinarum (Manilla clam) sRNA-seq Data from Azenta Project 30-1035633055

2024
Data Received
sRNA-seq
30-1035633055
Ruditapes philippinarum
Manila clam
The sRNA-seq data from Mac’s Manila clam egg samples submitted on 20240722 (Notebook) became available today. Data was downloaded to Owl and is available here:
Oct 1, 2024
Sam White

MD5 checksum verification 01

Data Received - E5 Coral Time Series RNA-seq Azenta Project 30-1047560508

2024
E5
coral
RNA-seq
30-1047560508
Azenta
Data Received
Coral time series RNA-seq data for Azenta project 30-1047560508 became availalbe today. Data was downloaded to nigthingales on Owl and MD5 checksums were verified.
Sep 26, 2024
Sam White

O'GeneRuler

Agarose Gel - gDNA Integrity Check of Lake Trout Liver gDNA from 20240712

2024
agarose gel
gDNA
Lake trout
liver
Salvelinus namaycush
After a previous attempt at amplifying the C1q gene in bisulfite-converted DNA failed, we decided we should test out a standard PCR on untreated liver gDNA. I designed PCR…
Sep 25, 2024
Sam White

PCR - Lake Trout C1Q with Liver gDNA

2024
PCR
Lake trout
C1q
CFX Connect
EpiMark Hot Start Taq
gDNA
liver
Salvelinus namaycush
After a previous attempt at amplifying the C1q gene in bisulfite-converted DNA failed, we decided we should test out a standard PCR on untreated liver gDNA. I designed PCR…
Sep 24, 2024
Sam White
 

Primer Design - Lake Trout C1q Gene Sequencing Primers Using Primer3

2024
C1q
lake trout
Salvelinus namaycush
Primer3
primer design
EMBOSS
pyfaidx
This notebook describes using Primer3 (Untergasser et al. 2012; Koressaar and Remm 2007) to reproducibly design primers for sequencing of the lake trout (S.namaycush) (Wikipe…
Sep 16, 2024
Sam White

PCR cycling parameters.

Bisulfite PCR - Second Primer Annealing Gradient Test with Lake Trout Bisulfite-treated DNA

2024
bisulfite
BS-PCR
PCR
DNA
Lake troute
Salvelinus namaycush
After previously designing bisulfite PCR primers for the C1Q gene on 20240709, and then screwing up the initial PCR, it was time to redo this the correct way. Due to their…
Sep 11, 2024
Sam White

MD5 checksum verification for first set of files.

Data Received - G.macrocephalus Supplemental RNA-seq Data from Azenta Project 30-943133806

Data Received
2024
Gadus macrocephalus
Pacific cod
RNA-seq
Azenta
We’d previously received RNA-seq data from Azenta on 2024-02-21. However, Laura realized that there was a large discrepancy between the amount of reads returned between…
Sep 9, 2024
Sam White
 

Daily Bits - September 2024

Daily Bits
2024
Confirmed MD5s for supplemental Pacific cod RNA-seq (Notebook).
Sep 3, 2024
Sam White

Snapped microfuge tube lid/neck.

DNA and RNA Isolations - Gadus macrocephalus Blood

2024
DNA isolation
RNA isolation
Gadus macrocephalus
Pacific cod
blood
Zymo Quick-DNA/RNA Miniprep
Qubit 3.0
Qubit DNA BR Assay
Qubit RNA HS Assay
Continued some testing samples for the Pacific cod project. In this instance, Steven and Laura asked that I extract DNA and RNA from the same blood sample (GitHub Issue).…
Aug 29, 2024
Sam White

PCR cycling parameters.

Bisulfite PCR - Testing Primer Annealing Gradient with Lake Trout Bisulfite-treated DNA

2024
BS-PCR
bisulfite
PCR
DNA
Lake trout
Salvelinus namaycush
This PCR was done incorrectly! The cycling program was setup incorrectly. Notebook post is being left for posterity.
Aug 28, 2024
Sam White

Bisulfite Conversion - Lake Trout gDNA Using EZ DNA Methylation Lightning Kit

2024
lake trout
Salvelinus namaycush
bisulfite
EZ DNA Methylation Lightning Kit
After isolating gDNA on 20240712 (Notebook), the next step was to perform bisulfite conversion.
Aug 13, 2024
Sam White
Empty chair with computer on a desk, surrouned by test tubes and beakers in a lab.

Daily Bits - August 2024

2024
Daily Bits
Reviewed lab safety inspection report. Fixed some deficiencies.
Aug 1, 2024
Sam White

Primer Design - Lake Trout C1q Gene Bisulfite Sequencing Primers Using Primer3

2024
C1q
lake trout
Salvelinus namaycush
Primer3
primer design
This notebook describes using Primer3 (Untergasser et al. 2012; Koressaar and Remm 2007) to reproducibly design primers for sequencing of the lake trout (S.namaycush) (Wikipe…
Jul 29, 2024
Sam White

Samples Submitted - Macs Manilla Clam Egg Samples for sRNA-seq at Azenta

2024
Samples Submitted
Azenta
sRNA-seq
Manila clam
Lajonkairia lajonkairii
Ruditapes philippinarum
eggs
Submitted the Manila clam egg samples Mac provided on 20240604 to Azenta for sRNA-seq.
Jul 22, 2024
Sam White

Gel image showing DNA ladder and high molecular weight bands for each of the four samples run. Sample 65B in Lane 4 appears to have a remarkably high band that has barely left the well.

DNA Isolation Quantification and Integrity Assessment - Pacific Cod Blood Samples Test

2024
Pacific cod
Gadus macrocephalus
DNA isolation
DNA quantification
Qubit
DNA BR Assay
agarose gel
Steven asked that I isolate gDNA from a Pacific cod blood samples (GitHub Issue). As we haven’t isolated gDNA from blood before, Laura Spencer identified a set of samples…
Jul 18, 2024
Sam White
 

DNA Isolation and Quantification - Pacific Cod Blood

2024
Pacific cod
Gadus macrocephalus
blood
DNA isolation
DNA quantification
Qubit
DNA BR assay
Steven asked that I isolate gDNA from a Pacific cod blood samples (GitHub Issue). Laura Spencer identified a set of samples (GitHub Issue). Below is the list of samples I…
Jul 18, 2024
Sam White

DNA Isolation and Quantification - Lake Trout Liver

DNA isolation
2024
lake trout
Salvelinus namaycush
Qubit
DNA BR assay
Steven asked that I isolate gDNA from a subset of lake trout (S.namaycush) liver samples (GitHub Issue) to use for targeted DNA methylation analyses via qPCR.
Jul 12, 2024
Sam White

Samples Received - L.staminea Histology Slides for Mac

2024
Leukoma staminea
littleneck clam
histology
slides
Samples Received
I retrieved histology slides (and cassettes) from the UW histology facility for Mac
Jul 9, 2024
Sam White

Daily Bits - July 2024

2024
Daily Bits
Took care of some administrative tasks related to tomorrow’s EH&S Lab Safety Inspection.
Jul 1, 2024
Sam White

RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024
project-lifestage-carryover
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
RNA HS assay
Qubit
RNA isolation
RNA quantification
Directzol RNA miniprep
I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…
Jul 1, 2024
Sam White

RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024
project-lifestage-carryover
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
RNA HS assay
Qubit
RNA isolation
Directzol RNA Miniprep
I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…
Jun 28, 2024
Sam White

RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024
project-lifestage-carryover
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
RNA HS assay
Qubit
RNA isolation
Directzol RNA Miniprep
I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…
Jun 27, 2024
Sam White

RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024
project-lifestage-carryover
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
RNA HS assay
Qubit
RNA isolation
Directzol RNA Miniprep
I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…
Jun 26, 2024
Sam White

RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024
project-lifestage-carryover
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
RNA HS assay
Qubit
RNA isolation
Directzol RNA Miniprep
I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…
Jun 25, 2024
Sam White

RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024
project-gigas-carryover
Crassostrea gigas
Pacific oyster
adult
seed
spat
Directzol RNA Miniprep
Qubit
RNA HS Assay
I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…
Jun 24, 2024
Sam White
 

HDD RMA - Failed Gannet HDD from 20240615

gannet
HDD
Synology
Sent bad Gannet HDD identified on 20240616 back to Amazon vendor (Maestro Technologies), using the supplied RMA shipping label. Drive will be replaced at their cost.
Jun 24, 2024
Sam White
 

RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024
project-gigas-carryover
Crassostrea gigas
Pacific oyster
adult
seed
spat
Directzol RNA Miniprep
Qubit
RNA HS assay
I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…
Jun 18, 2024
Sam White

Histology cassettess in drop off area.

Samples Submitted - Littleneck Clam Histology Cassettes to UW Pathology Research Services Laboratory

2024
histology
littleneck clam
Pathology Research Services Laboratory
Samples Submitted
Mac requested I dop off some littleneck clam histology cassettes (GitHub Issue) at the UW Pathology Research Services Laboratory (HSB C411).
Jun 18, 2024
Sam White
 

RNA Quantification - C.gigas RNA Lifestage Carryover from 20240615 and 20240617

2024
project-gigas-carryover
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
Qubit
RNA HS assay
I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…
Jun 17, 2024
Sam White
 

RNA Isolation - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024
project-gigas-carryover
Directzol RNA Miniprep
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…
Jun 17, 2024
Sam White
 

RNA Isolation - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024
project-gigas-carryover
Directzol RNA Miniprep
Crassostrea gigas
Pacific oyster
seed
adult
juvenile
I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…
Jun 15, 2024
Sam White

Computer Maintenance - Replace Bad HDD on Gannet

computer maintenance
2024
HDD
gannet
synology
Hard drive recently failed (showed “Critical” status in Synology Storage Manager). Replaced the drive with a new one. Checking the serial number on Seagate’s website…
Jun 15, 2024
Sam White

Volcano plost of differentialy expressed genes. More highly expressed in 9C are red, while those more highly expressed in 16C are blue. Both groups are > 1 fold log change and < -1 log fold change, respectively. Mustard yellow dots represent differentially expressed genes between -1 and 1 fold log change.

Differential Gene Expression - G.macrocephalus RNA-seq 9C vs 16C Using edgeR

edgeR
Pacific cod
RNA-seq
differential gene expression
2024
Gadus macrocephalus
Differential gene expression of 9oC vs 16oC liver RNA-seq using edgeR (Chen et al. 2024; McCarthy, Chen, and Smyth 2012; Chen, Lun, and Smyth 2016; Robinson, McCarthy, and…
Jun 11, 2024
Sam White

Egg samples box

Samples Received - Lajonkairia lajonkairii Egg Samples from Mackenzie Gavery

Lajonkairia lajonkairii
manilla clam
2024
Samples Received
Went to NOAA (NWFSC) to get Manilla clam (Lajonkairia lajonkairii) egg samples from Mac for an RNA-seq project.
Jun 4, 2024
Sam White
 

Daily Bits - June 2024

Daily Bits
2024
Isolated and quantified RNA (Notebook) for `project-lifestage-carryover project (GitHub repo).
Jun 1, 2024
Sam White

Gel with untouched samples on left.

Agarose Gel - G.macrocephalus gDNA from 20240521

agarose
gDNA
Gadus macrocephalus
Pacific cod
gel
2024
Previously isolated and quantified gDNA on 20240531 (Notebook) and needed to evaluate gDNA integrity. We recently sent a bunch of liver samples off to Psomagagen for whole…
May 31, 2024
Sam White
 

DNA Isolation - Pacific cod liver

DNA isolation
Pacific cod
liver
Gadus macrocephalus
DNA quantification
Qubit
2024
We recently sent a bunch of liver samples off to Psomagagen for whole genome bisulfite sequencing (WGBS). As documented in this GitHub Issue, Psomagen discovered that the…
May 21, 2024
Sam White
 

Daily Bits - May 2024

Daily Bits
2024
Ran G.macrocephalus gDNA on a gel.
May 1, 2024
Sam White
 

Samples Submitted - Pacific Cod 40 Tissue Samples for WGBS at Psomagen

psomagen
WGBS
2024
Pacific cod
Gadus macrocephalus
BS-seq
bisulfite
Samples Submitted
Submitted 40 Gadus macrocephalus tissue/blood samples (GitHub Issue) to Psomagen for gDNA isolation and whole genome bisulfite sequencing (WGBS).
Apr 30, 2024
Sam White

Screenshot of Storage Manager showing drives as “Detected”

Computer Troubleshooting - Gannet Missing Storage Pool

gannet
Synology
server
2024
Most of this stuff is addressed in this GitHub Issue, but here’s the summary:
Apr 23, 2024
Sam White
 

Daily Bits - April 2024

daily bits
2024
Helped Eric get started with qPCR analysis.
Apr 1, 2024
Sam White

Box plots comparing GAPDH-normalized gene expression (delta Cq) between control and treated seed. Blue boxes are treated and red boxes are control. HSP90 is the only gene showing higher expression in treated samples. However, none of the differences in gene expression between controls and treated showed any statistically significant (t-test) differences.

qPCR Analysis - C.gigas Lifestages Carryover from 20240325

2024
qPCR
Crassotrea gigas
Pacific oyster
qPCR analysis of Crassostrea gigas (Pacific oyster) spat and seed from the project-gigas-carryover (GitHub Repo).
Mar 27, 2024
Sam White

ATPsynthase amplification plots

qPCRs - C.gigas Lifestage Carryover cDNA

qPCR
SsoFast
CFX Connect
HSP70
HSP90
GAPDH
VIPERIN
ATPsynthase
cGAS
DMNT1
citrate synthase
Crassostrea gigas
Pacific oyster
cDNA
Ran qPCRs on the cDNA I made last week (Notebook), as part of the project-gigas-carryover (GitHub Repo). This file provides metadata for the samples being qPCR’d:
Mar 25, 2024
Sam White

Box with blue label: Lifestage Carryover, C.gigas cDNA Box #1

Reverse Transcription - C.gigas Lifestage Carryover Seed and Spat

reverse transcription
Lifestage carryover
Crassostrea gigas
Pacific oyster
cDNA
M-MLV
2024
After isolating RNA earlier today (Notebook) for the project-gigas-carryover/lifestage_carryover (GitHub repo), I proceeded with reverse transcription for those samples with…
Mar 19, 2024
Sam White
 

RNA Isolation - C.gigas Lifestage Carryover Seed and Spat

RNA isolation
Crassostrea gigas
Lifestage carryover
Pacific oyster
2024
I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat and seed that had been collected as part of the proj…
Mar 19, 2024
Sam White
 

SRA Submission - CEABIGR WGBS and RNA-seq

SRA
CEABIGR
Crassostrea virginica
Eastern oyster
RNAseq
WGBS
2024
Finally got around to getting the CEABIGR (GitHub repo) sequencing data uploaded to NCBI’s Short Read Archive (SRA). Data transfer took quite awhile, as we have both whole…
Mar 18, 2024
Sam White

Oysters in 12-well plate, a ruler, and oysters in two glass Petri dishes.

Resazurin - C.gigas Second Trial

Crassostrea gigas
Pacific oyster
2024
resazurin
After running the initial resazuring test on 20240308 (Notebook), Steven/Ariana asked that I run another trial (GitHub Issue). This second trial was designed to get some…
Mar 12, 2024
Sam White

Resazurin - Preliminary Respiration Test Using C.gigas

resazurin
Crassostrea gigas
Pacific oyster
2024
We’re beginning to gather some preliminary data for a project examining the effects of “stress priming” on _Crassostrea gigas (Pacific oyster). GitHub repo is here. As part…
Mar 8, 2024
Sam White
 

Daily Bits - March 2024

2024
Daily Bits
Isolated RNA for gigas carryover project (Notebook)
Mar 1, 2024
Sam White

Screenshot showing MD5 checksum verification of FastQ files.

Data Received - Pacific cod RNA-seq Azenta Project 30-943133806

Azenta
RNA-seq
2024
Pacific cod
Gadus macrocephalus
30-943133806
Data Received
Received Pacific cod liver/gill/spleen RNA-seq data back from Azenta today (project 30-943133806). Files were downloaded to Owl and MD5 checksums were verified. The Nightinga…
Feb 21, 2024
Sam White
 

sRNA-seq Paired Read Merging Explorations - Coral E5 Deep Dive

2024
E5
sRNA-seq
merge
bbmerge
fastp
Our previous sRNA-seq data analysis for this project revealed that the R2 reads didn’t seem to match with anything (specifically, no clade assignments when using miRTrace)…
Feb 2, 2024
Sam White
 

Daily Bits - February 2024

2024
Daily Bits
Finalized females/males controls/exposed expression table.
Feb 1, 2024
Sam White

Line plots of mean natural log fold-change of exon expression relative to Exon 1. Pink line is control females. Blue line is control males. Black bars represent standard error.

Figure Updates - CEABIGR Spurious Transcription Calcs and Plotting Using Exon Sum Threshold

CEABIGR
2024
plot
Eastern oyster
Crassostrea virginica
As part of the CEABIGR project (GitHub repo) Steven performed some inital data wrangling to test out the basic calculations to determine the natural log of the fold change…
Jan 24, 2024
Sam White

Line plots of mean natural log fold-change of exon expression relative to Exon 1. Pink line is control females. Blue line is control males. Black bars represent standard error.

Data Exploration - CEABIGR Spurious Transcription Calculations and Plotting

2024
CEABIGR
plot
Eastern oyster
Crassostrea virginica
As part of the CEABIGR project (GitHub repo) Steven performed some inital data wrangling to test out the basic calculations to determine the natural log of the fold change…
Jan 3, 2024
Sam White
 

Daily Bits - January 2024

2024
Daily Bits
Helped Chris troubleshoot her SOD assay standard curve. She felt like her samples SOD activity was too low and falling outside of the standard curve.
Jan 2, 2024
Sam White
 

Computer Management - Returned Failing HDDs from Gannet Expansion Unit

computer management
2023
HDDs
gannet
After replacing the three failing HDDs in the Gannet (Synology) expansion unit, I contacted the company (Maestro Technology LLC) via Amazon. They have been very responsive…
Dec 21, 2023
Sam White
 

Samples Submitted - Gadus macrocephalus liver tissues to Azenta for RNA-seq

2023
Gadus macrocephalus
Pacific cod
Azenta
RNA-seq
Samples Submitted
liver
spleen
gill
blood
Shipped box of 80 Pacific cod tissues selected by Steven (mostly liver, some blood, gills, and spleen) to Azenta overnight on dry ice for RNA-seq.
Dec 18, 2023
Sam White

Synology logs showing three drives failing S.M.A.R.T. tests

Computer Maintenance - Replace Failing HDDs in Synology RX1217 Expansion Unit on Gannet

gannet
synology
RX1217
HDDs
2023
computer maintenance
In mid-Novemeber, our Synology RX1217 expansion unit on Gannet generated erros for three drives. Considering this unit, and the corresponding HDDs, were installed in July…
Dec 7, 2023
Sam White
 

Data Investigation - Mysterious Case of Excessive Exons in CEABIGR

CEABIGR
Crassostrea viriginica
Eastern oyster
2023
After Steven ran through some prelimiary exon expression analyses (GitHub Isse), he noticed that there were some genes with a seemingly excessive number of exons (like over…
Dec 6, 2023
Sam White
 

Daily Bits - December 2023

Daily Bits
Read Ch.3 of “Race After Technology: The New Jim Code”
Dec 1, 2023
Sam White

Plotting Fun - Lab Meeting Task

plotting
R
For today’s lab meeting, Steven tasked us with the following on Wednesday:
Nov 30, 2023
Sam White

Transcriptome Annotation - M.magister De Novo Transcriptome Assembly Using Trinotate on Mox

mox
2023
Metacarcinus magister
Dungenss crab
Trinotate
transcriptome
annotation
As part of transcriptome annotation (GitHub issue) for DuMOAR (GitHub repo), I’ve already run TransDecoder ( run on 20231107), as well as DIAMOND BLASTx (run earlier today).…
Nov 9, 2023
Sam White

Transcriptome Annotation - M.magister De Novo Transcriptome Assembly for DuMOAR Project Using DIAMOND BLASTx on Mox

mox
DIAMOND
BLASTx
transcriptome
2023
DuMOAR
Dungeness crab
Metacarcinus magister
As part of the process for using Trinotate for transcriptome annotation (GitHub Issue), I previously ran TransDecoder on 20231107. Next, I needed to run BLASTx. As usual, I…
Nov 9, 2023
Sam White
 

Daily Bits - November 2023

Daily Bits
2023
Lab meeting.
Nov 5, 2023
Sam White
 

qPCR Analysis - C.gigas Matt George PolyIC Diploids

qPCR
CFX Connect
Crassostrea gigas
diploid
Pacific oyster
2023
Miscellaneous
Ran a “quick and dirty” qPCR analysis for the qPCR’s I’d previously run:
Aug 22, 2023
Sam White
 

Transcript Identification and Alignments - C.virginica RNAseq with NCBI Genome GCF_002022765.2 Using Hisat2 and Stringtie on Mox Again

2023
Miscellaneous
In the process of generating expression matrices for CEABIGR (GitHub repo), and in turn distance matrices for these samples, I realized a couple of things:
Aug 21, 2023
Sam White
 

qPCR - C.gigas PolyIC Diploid MgCl2

2023
Miscellaneous
Using diploid MgCl2 control cDNA from 20230816, performed qPCR on the following primer sets selected by Steven (GitHub Issue), along with Cg_Actin as a potential normalizing…
Aug 17, 2023
Sam White
 

Reverse Transcription - C.gigas PolyIC Diploid MgCl2

2023
Miscellaneous
After quantifying diploid MgCl2 (Notebook) earlier today and proceeded to make cDNA. Reverse transcription was performed using oligo dT primers using M-MLV RT (Promega), per…
Aug 16, 2023
Sam White
 

RNA Quantification - C.gigas PolyIC Diploid MgCl2

2023
Miscellaneous
Steven asked me to generate cDNA (GitHub Issue) from Crassostrea gigas (Pacific oyster) RNA, as part of Matt George’s polyIC project. I had previously quantified RNA from…
Aug 16, 2023
Sam White
 

Daily Bits - August 2023

2023
Daily Bits
20230830
Aug 1, 2023
Sam White
 

sRNA-seq Alignments - E5 Coral P.evermanni Using ShortStack on Mox

2023
E5
Steven asked that I run ShortStack on the E5 P.evermanni sRNA-seq (GitHub Issue) data we had. I used trimmed sRNA-seq reads from 20230620 (notebook entry) and the P.evermanni…
Jul 31, 2023
Sam White
 

Read Extractions - M.magister MEGAN FastA to FastQ Arthropoda and Unassigned Reads

2023
DuMOAR
After getting Arthropoda and Unassigned reads extracted to FastA format (notebook entry) using MEGAN6 Community Edition, the next step was to use the FastA files to extract…
Jul 30, 2023
Sam White
 

DIAMOND BLASTx - C.virginica Genes on Mox

2023
CEABIGR
As part of annotating Ballgown transcripts for this project, I generated a genes FastA file on 20230726 (notebook entry). The next aspect of the annotation process was to…
Jul 27, 2023
Sam White
 

qPCR - C.gigas polyIC

2023
Miscellaneous
Using cDNA from 20230721, performed qPCR on the following primer sets selected by Steven (GitHub Issue), along with Cg_Actin as a potential normalizing gene:
Jul 26, 2023
Sam White
 

Data Wrangling - C.virginica Genes Only FastA from Genes BED File Using gffread on Raven

2023
CEABIGR
I’ve been reviewing some of the CEABIGR (GitHub repo) data I’ve generated; specifically transcript count data/calcs. As part of that, I feel like we need/should annotate the…
Jul 26, 2023
Sam White
 

Read Extractions - M.magister MEGAN Arthropoda and Unassigned Reads to FastA

2023
DuMOAR
After converting DIAMOND BLASTx/MEGAN DAA files to RMA6 and looking at the taxonomic breakdown of each sample (notebook entry), it was decided we should extract reads from Ar…
Jul 26, 2023
Sam White
 

RNA Quantification - C.gigas PolyIC

2023
Miscellaneous
Steven asked me to generate cDNA (GitHub Issue) from Crassostrea gigas (Pacific oyster) RNA, as part of Matt George’s polyIC project. Before starting reverse transcription…
Jul 21, 2023
Sam White
 

Reverse Transcription - C.gigas PolyIC RNA

2023
Miscellaneous
Quantified RNA earlier today and proceeded to make cDNA. Reverse transcription was performed using oligo dT primers using M-MLV RT (Promega), per the manufacturer’s…
Jul 21, 2023
Sam White
 

qPCR - C.gigas Ctenidia cDNA for Noah's Heat-Mechanical Stress Project

2023
Miscellaneous
Using cDNA from 20230713, performed qPCR on the following primer sets selected by Steven:
Jul 21, 2023
Sam White
 

qPCR - C.gigas Ctenidia cDNA for Noah's Heat-Mechanical Stress Project

2023
Miscellaneous
Using cDNA from 20230713, performed qPCR on the following primer sets selected by Steven:
Jul 19, 2023
Sam White
 

qPCR - C.gigas cDNA Primer Tests for Noah's Heat-Mechanical Stress Project

2023
Miscellaneous
After generating cDNA earlier today from Noah’s Crassostrea gigas (Pacific oyster) RNA (isolated 20230712), I ran qPCRs using the pooled cDNA sample to test out some primers…
Jul 13, 2023
Sam White
 

Reverse Transcription - C.gigas RNA from Noah's Heat-Mechanical Stress Project

2023
Miscellaneous
After isolating ctenidia RNA on 20230712 and then quantifying the RNA earlier today, I needed to perform reverse transcription to have cDNA for subsequent qPCRs. Reverse…
Jul 13, 2023
Sam White
 

RNA Quantification - C.gigas RNA from Noah's Heat-Mechanical Stress Project

2023
Miscellaneous
I quantified Noah’s Crassostrea gigas (Pacific oyster) ctenidia RNA from yesterday (20230712) using the Roberts Lab Qubit 3 and the RNA High Sensitivity (HS) Assay. 1uL of…
Jul 13, 2023
Sam White
 

RNA Isolation - C.gigas Ctenidia from Noah's Heat-Mechanical Stress Project

2023
Miscellaneous
Steven asked that I help isolate RNA (GitHub Issue) for Noah’s summer project involving heat and mechanical stress (tumbling) of adult Crassostrea gigas (Pacific oyster).…
Jul 12, 2023
Sam White
 

Daily Bits - July 2023

2023
Daily Bits
20230726
Jul 5, 2023
Sam White
 

File Conversion - M.magister MEGANized DAA to RMA6

2023
Miscellaneous
After the initial DIAMOND BLASTx and subsequent MEGANization(notebook) ran for 41 days, I attempted to open the extremely large files in the MEGAN6 GUI to get an overview of…
Jul 2, 2023
Sam White
 

Data Received - Pacific Cod (G.macrocephalus) Sequencing Data from Novogene

2023
Data Received
Downloaded Pacific cod (_G.macrocephalus) sequencing data. I believe this is a NOAA project, and I don’t have any info about it. So, not much to report here.
Jun 30, 2023
Sam White
 

sRNA-seq Alignments - E5 Coral A.pulchra P.meandrina Using ShortStack on Mox

2023
E5
Steven had asked that I align the coral E5 sRNA-seq reads using ShortStack (GitHub Issue). I previously trimmed the sRNA-seq reads to 35bp in length (notebook). Next up was…
Jun 28, 2023
Sam White
 

Trimming and QC - E5 Coral sRNA-seq Data fro A.pulchra P.evermanni and P.meandrina Using FastQC flexbar and MultiQC on Mox

2023
E5
After downloading (notebook) and then reorganizing the E5 coral RNA-seq data from Azenta project 30-789513166 (notebook), and after testing some trimming options for…
Jun 20, 2023
Sam White
 

ORF Identification - L.staminea De Novo Transcriptome Assembly v1.0 Using Transdecoder on Mox

2023
Miscellaneous
After performing a de novo transcriptome assembly with L.staminea RNA-seq data, the Trinity assembly stats were quite a bit more “exaggerated” than normally expected. In an…
Jun 17, 2023
Sam White
 

Transcriptome Assembly - De Novo L.staminea Trimmed RNAseq Using Trinity on Mox

2023
Miscellaneous
As part of this GitHub Issue to create a de novo transcriptome assembly from L.staminea RNA-seq data, I trimmed the reads earlier today. Next up is the actual do novo assembl…
Jun 16, 2023
Sam White
 

Trimming - L.staminea RNA-seq Using FastQC fastp and MultiQC on Mox

2023
Miscellaneous
Per this GitHub Issue, Steven asked me to perform a de novo transcriptome assembly on one set of paired FastQ from some little neck clam (L.staminea) RNA-seq. Prior to…
Jun 16, 2023
Sam White
 

Daily Bits - June 2023

2023
Daily Bits
20230605
Jun 2, 2023
Sam White
 

Repeats Identification - P.meandrina Using RepeatMasker on Mox

2023
E5
Steven asked me to run RepeatMasker on the P.meandrina genome (GitHub Issue) for eventual use in developing a count matrix for transposable elements. The P.meandrina genome…
May 26, 2023
Sam White
 

Trimming and QC - E5 Coral sRNA-seq Trimming Parameter Tests and Comparisons

2023
E5
In preparation for FastQC and trimming of the E5 coral sRNA-seq data, I noticed that my “default” trimming settings didn’t produce the results I expected. Specifically…
May 24, 2023
Sam White
 

Data Wrangling - P.meandrina Genome GFF to GTF Using gffread

2023
E5
As part of getting P.meandrina genome info added to our Lab Handbook Genomic Resources page, I will index the P.meandrina genome file (Pocillopora_meandrina_HIv1.assembly.fas…
May 19, 2023
Sam White
 

FastQ QC and Trimming - E5 Coral RNA-seq Data for A.pulchra P.evermanni and P.meandrina Using FastQC fastp and MultiQC on Mox

2023
E5
After downloading and then reorganizing the E5 coral RNA-seq data from Azenta project 30-789513166, I ran FastQC for initial quality checks, followed by trimming with fastp…
May 19, 2023
Sam White
 

Data Management - E5 Coral RNA-seq and sRNA-seq Reorganizing and Renaming

2023
Data Management
Downloaded the E5 coral sRNA-seq data from Azenta project 30-852430235 on 20230515 and the E5 coral RNA-seq data from Azenta project 30-789513166 on 20230516. The data…
May 17, 2023
Sam White
 

Data Received - Coral RNA-seq Data from Azenta Project 30-789513166

2023
Data Received
Small RNA-seq (sRNA-seq) data was made available from the coral E5 Azenta project 30-789513166. Sample sheet:
May 16, 2023
Sam White
 

Data Received - Coral sRNA-seq Data from Azenta Project 30-852430235

2023
Data Received
Small RNA-seq (sRNA-seq) data was made available from the coral E5 Azenta project 30-852430235. Sample sheet is below.
May 15, 2023
Sam White
 

lncRNA Expression - P.generosa lncRNA Expression Using StringTie

2023
Miscellaneous
After identifying lncRNA in P.generosa, Steven asked that I generate an tissue-specific expression/count matrix (GitHub Issue). Looking through the documentation for StringTie…
May 4, 2023
Sam White
 

Daily Bits - May 2023

2023
Daily Bits
20230517
May 2, 2023
Sam White
 

lncRNA Identification - P.generosa lncRNAs using CPC2 and bedtools

2023
Miscellaneous
After trimming P.generosa RNA-seq reads on 20230426 and then aligning and annotating them to the Panopea-generosa-v1.0 genome on 20230426, I proceeded with the final step of…
May 2, 2023
Sam White
 

Containers - Apptainer Explorations

2023
Miscellaneous
At some point, our HPC nodes on Mox will be retired. When that happens, we’ll likely purchase new nodes on the newest UW cluster, Klone. Additionally, the coenv nodes are no…
Apr 28, 2023
Sam White
 

Transcript Alignments - P.generosa RNA-seq Alignments for lncRNA Identification Using Hisat2 StingTie and gffcompare on Mox

2023
Miscellaneous
This is a continuation of the process for identification of lncRNAs,. I aligned FastQs which were previously trimmed earlier today to our Panopea-generosa-v1.0 genome FastA…
Apr 26, 2023
Sam White
 

FastQ Trimming and QC - P.generosa RNA-seq Data from 20220323 on Mox

2023
Miscellaneous
Addressing the update to this GitHub Issue regarding identifying Panopea generosa (Pacific geoduck) long non-coding RNAs (lncRNAs), I used the RNA-seq data from the Nextflow…
Apr 26, 2023
Sam White
 

Data Wrangling - CEABIGR C.virginica Exon Expression Table

2023
CEABIGR
As part of the CEABIGR project (GitHub repo), Steven asked that I generate an exon expression table (GitHub Issue) where each row is a gene and the columns are the…
Apr 5, 2023
Sam White
 

Daily Bits - April 2023

2023
Daily Bits
20230403
Apr 3, 2023
Sam White
 

Data Wrangling - Append Gene Ontology Aspect to P.generosa Primary Annotation File

2023
Miscellaneous
Steven tasked me with updating our P.generosa genome annotation file (GitHub Issue) a while back and I finally managed to get it all figured out. Although I wanted to…
Mar 29, 2023
Sam White
 

Sequencing Read Taxonomic Classification - M.magister RNA-seq Using DIAMOND BLASTx and MEGAN6 daa-meganizer on Mox

2023
Miscellaneous
Running DIAMOND BLASTx, followed by MEGAN6 daa-meganizer for taxonomic classification of NOAA M.magister trimmed RNA-seq reads (provided by Giles Goetz on 20230301). This is…
Mar 16, 2023
Sam White
 

Daily Bits - March 2023

2023
Daily Bits
20230329
Mar 3, 2023
Sam White
 

Data Received - Trimmed M.magister RNA-seq from NOAA

2023
Data Received
Transferred trimmed C.magister RNA-seq data from Google Drive to our HPC (Mox) using rclone. This was a great suggestion from Giles Goetz!
Mar 1, 2023
Sam White
 

Sequencing Read Taxonomic Classification - P.verrucosa E5 RNA-seq Using DIAMOND BLASTx and MEGAN daa-meganizer on Mox

2023
E5
After some discussion with Steven at Science Hour last week regarding the handling of endosymbiont sequences in the E5 P.verrucosa RNA-seq data, Steven thought it would be…
Feb 21, 2023
Sam White
 

Data Wrangling - C.goreaui Genome GFF to GTF Using gffread

2023
E5
As part of getting these three coral species genome files (GitHub Issue) added to our Lab Handbook Genomic Resources page, I also need to get the coral endosymbiont…
Feb 17, 2023
Sam White
 

Transcript Identification and Alignments - P.verrucosa RNA-seq with Pver_genome_assembly_v1.0 Using HiSat2 and Stringtie on Mox

2023
E5
After getting the RNA-seq data trimmed, it was time to perform alignments and determine expression levels of transcripts/isoforms using with HISAT2 and StringTie…
Feb 16, 2023
Sam White
 

FastQ Trimming and QC - P.verrucosa RNA-seq Data from Danielle Becker in Hollie Putnam Lab Using fastp FastQC and MultiQC on Mox

2023
E5
After receiving the P.verrucosa RNA-seq data from Danielle Becker (Hollie Putnam’s Lab, Univ. of Rhode Island), I noticed that the trimmed reads didn’t appear to actually be…
Feb 15, 2023
Sam White
 

Data Wrangling - Create P.verrucosa GCA_014529365.1 Karyotype File

2023
E5
Steven asked that I create a karyotype file (GitHub Issue) from the NCBI P.verrucosa genome (GCA_014529365.1) in the following format:
Feb 15, 2023
Sam White
 

Data Received - P.verrucosa RNA-seq and WGBS Full Data from Danielle Becker

2023
E5
Data Received
Worked with Danielle Becker, as part of the Coral E5 project, to transfer data related to her repo, from her HPC (Univ. of Rhode Island; Andromeda) to ours (Univ. of…
Feb 10, 2023
Sam White
 

Daily Bits - February 2023

2023
Daily Bits
20230223
Feb 1, 2023
Sam White
 

Genome Indexing - P.verrucosa v1.0 Assembly with HiSat2 on Mox

2023
Miscellaneous
Working on this Issue regarding adding coral genomes to our Handbook (GitHub) and needed to generate a HISAT2 index to add to The Roberts Lab Handbook Genomic Resources.
Jan 31, 2023
Sam White
 

Genome Indexing - M.capitata HIv3 Assembly with HiSat2 on Mox

2023
Miscellaneous
Working on this Issue regarding adding coral genomes to our Handbook (GitHub) and needed to generate a HISAT2 index to add to The Roberts Lab Handbook Genomic Resources.
Jan 31, 2023
Sam White
 

Genome Indexing - P.acuta HIv2 Assembly with HiSat2 on Mox

2023
Miscellaneous
Working on this Issue regarding adding coral genomes to our Handbook (GitHub) and needed to generate a HISAT2 index to add to The Roberts Lab Handbook Genomic Resources.
Jan 31, 2023
Sam White
 

Data Wrangling - P.verrucosa Genome GFF to GTF Using gffread

2023
Miscellaneous
As part of getting these three coral species genome files (GitHub Issue) added to our Lab Handbook Genomic Resources page, I will index the P.verrucosa genome file (Pver_geno…
Jan 27, 2023
Sam White
 

Data Wrangling - M.capitata Genome GFF to GTF Using gffread

2023
Miscellaneous
As part of getting these three coral species genome files (GitHub Issue) added to our Lab Handbook Genomic Resources page, I will index the M.capitata genome file (Montipora_…
Jan 27, 2023
Sam White
 

Data Wrangling - P.acuta Genome GFF to GTF Conversion Using gffread

2023
Miscellaneous
As part of getting these three coral species genome files (GitHub Issue) added to our Lab Handbook Genomic Resources page, I will index the P.acuta genome file using HISAT2…
Jan 26, 2023
Sam White
 

Genome Indexing - P.verrucosa NCBI GCA_014529365.1 with HiSat2 on Mox

2023
Miscellaneous
Working on this Issue regarding adding coral genomes to our Handbook (GitHub) and needed to generate a HISAT2 index to add to The Roberts Lab Handbook Genomic Resources.
Jan 25, 2023
Sam White
 

Genome Indexing - M.capitata NCBI GCA_006542545.1 with HiSat2 on Mox

hisat2
Montipora capitata
coral
GCA_006542545.1
mox
2023
Miscellaneous
Working on this Issue regarding adding coral genomes to our Handbook (GitHub) and needed to generate a HISAT2 index to add to The Roberts Lab Handbook Genomic Resources.
Jan 25, 2023
Sam White
 

SRA Data - Coral SRA BioProject PRJNA744403 Download and QC

PRJNA744403
SRA
NCBI
fastp
FastQC
MultiQC
coral
metagenomics
2023
Miscellaneous
Per this GitHub Issue, Steven wanted me to download all of the SRA data (RNA-seq and WGBS-seq) from NCBI BioProject PRJNA744403 and run QC on the data.
Jan 13, 2023
Sam White
 

Monthly Goals - January 2023

2023
Monthly Goals
Plot CEABIGR coefficients of variation comparisons of mean gene methylation.
Jan 5, 2023
Sam White
 

Daily Bits - January 2023

2023
Daily Bits
20230131
Jan 3, 2023
Sam White
 

BS-Seq Analysis - Nextflow EpiDiverse SNP Pipeline for Haws Hawaii C.gigas BAMs from Yaamini Base Config

2022
Miscellaneous
Yaamini asked me to run the epidiverse/snp pipeline (GitHub Issue) on her Haws Crassostrea gigas (Pacific oyster) Hawaii bisuflite sequencing BAMs for SNP identification.
Dec 15, 2022
Sam White
 

BS-Seq Analysis - Nextflow EpiDiverse SNP Pipeline for Haws Hawaii C.gigas BAMs from Yaamini

2022
Miscellaneous
Yaamini asked me to run the epidiverse/snp pipeline (GitHub Issue) on her Haws Crassostrea gigas (Pacific oyster) Hawaii bisuflite sequencing BAMs for SNP identification.
Dec 14, 2022
Sam White
 

Daily Bits - December 2022

2022
Daily Bits
20221227
Dec 1, 2022
Sam White
 

Daily Bits - November 2022

2022
Daily Bits
20221121
Nov 1, 2022
Sam White
 

Daily Bits - October 2022

2022
Daily Bits
20221031
Oct 1, 2022
Sam White
 

Data Wrangling - C.virginica NCBI GCF_002022765.2 GFF to Gene and Pseudogene Combined BED File

2022
Miscellaneous
Working on the CEABIGR project, I was preparing to make a gene expression file to use in CIRCOS (GitHub Issue) when I realized that the Ballgown gene expression file (CSV;…
Sep 26, 2022
Sam White
 

BSseq SNP Analysis - Nextflow EpiDiverse SNP Pipeline for C.virginica CEABIGR BSseq data

2022
Miscellaneous
Steven asked that I identify SNPs from our C.virginica CEABIGR BSseq data (GitHub Issue). So, I ran sorted, deduplicated Bismark BAMs that Steven generated through the EpiDiv…
Sep 21, 2022
Sam White
 

Data Wrangling - Identify C.virginica Genes with Different Predominant Isoforms for CEABIGR

2022
CEABIGR
During today’s discussion, Yaamini recommended we generate a list of genes with different predominant isoforms between females and males, while also adding a column with a…
Sep 20, 2022
Sam White
 

RNAseq Alignments - P.generosa Alignments and Alternative Transcript Identification Using Hisat2 and StringTie on Mox

2022
Miscellaneous
As part of identifying long non-coding RNA (lncRNA) in Pacific geoduck(GitHub Issue), one of the first things that I wanted to do was to gather all of our geoduck RNAseq…
Sep 14, 2022
Sam White
 

FastQ Trimming - Geoduck RNAseq Data Using fastp on Mox

2022
Miscellaneous
Per this GitHub Issue, Steven asked me to identify long non-coding RNA (lncRNA) in geoduck. The first step is to aggregate all of our Panopea generosa (Pacific geoduck) RNAse…
Sep 8, 2022
Sam White
 

Daily Bits - September 2022

September
2022
Daily Bits
20220930
Sep 2, 2022
Sam White
 

FastQ Trimming and QC - C.virginica Larval BS-seq Data from Lotterhos Lab and Part of CEABIGR Project Using fastp on Mox

BSseq
Lotterhos
CEABIGR
Crassostrea virginica
Eastern oyster
fastp
mox
2022
Miscellaneous
The trimmming described below is probably incomplete and should be ignored.
Aug 29, 2022
Sam White
 

Data Wrangling - Convert S.namaycush NCBI GFF to genes-only BED file for Use in Ballgown Analysis

2022
Miscellaneous
In preparation for isoform identificaiton/quantification in S.namaycush RNAseq data, Ballgown will need a genes-only BED file. To generate, I used GFFutils to extract only…
Aug 18, 2022
Sam White
 

Splice Site Identification - S.namaycush Liver Parasitized and Non-Parasitized SRA RNAseq Using Hisat2-Stingtie with Genome GCF_016432855.1

2022
Miscellaneous
After previously downloading/trimming/QCing S.namaycush SRA liver RNAseq data on 20220706, Steven asked that I run through Hisat2 for splice site identification (GitHub…
Aug 10, 2022
Sam White
 

qPCR - Repeat of Mussel Gill Heat Stress cDNA with Ferritin Primers

2022
Miscellaneous
My previous qPCR on these cDNA using ferritin primers (SRIDs: 1808, 1809) resulted in no amplification. This was a bit surprising and makes me suspect that I screwed up…
Aug 4, 2022
Sam White
 

Daily Bits - August 2022

August
2022
Daily Bits
20220831
Aug 3, 2022
Sam White
 

qPCR - Dorothys Mussel cDNA from 20220726

2022
Miscellaneous
Ran qPCRs on Dorothy’s mussel gill cDNA from 20220726 using the following primers:
Jul 27, 2022
Sam White
 

RNA Isolation and Quantification - Dorothy Mussel Gill Samples

2022
Miscellaneous
Isolated RNA from a subset of Dorothy’s mussel gill samples:
Jul 26, 2022
Sam White
 

BS-seq and SNP Analysis - Nextflow EpiDiverse Pipelines Trials and Tribulations

2022
Miscellaneous
Alrighty, this notebook entry is going to have a lot to unpack, as the process to get these pipelines running and then deal with the actual data we wanted to run them with…
Jul 25, 2022
Sam White
 

SRA Data - S.namaycush SRA BioProject PRJNA674328 Download and QC

2022
Miscellaneous
Per this GitHub Issue, which I accidentally forgot about for three weeks (!), Steven wanted me to download the lake trout (Salvelinus namaycush) RNAseq data from NCBI…
Jul 6, 2022
Sam White
 

Daily Bits - July 2022

2022
Daily Bits
20220727
Jul 5, 2022
Sam White
 

Daily Bits - June 2022

2022
Daily Bits
20220624
Jun 22, 2022
Sam White
 

SRA Submission - Ostrea lurida MBD BS-seq from 20160203

2022
SRA Submission
Submitted our Ostrea lurida (Olympia oyster) MBD BS-seq data from 20160203 to the NCBI Sequence Read Archive (SRA).
Jun 15, 2022
Sam White
 

Project Summary - C.virginica CEABiGR - Female vs. Male Gonad Exposed to OA

Crassostrea virginica
CEABIGR
OA
gonad
Eastern oyster
2022
Project Summary
This will be a “dynamic” notebook entry, whereby I will update this post continually as I process new samples, analyze new data, etc for this project. The hope is to make it…
Apr 25, 2022
Sam White
 

Data Wrangling - Create Primary P.generosa Genome Annotation File

2022
Miscellaneous
Steven asked me to create a canonical genome annotation file (GitHub Issue). I needed/wanted to create a file containing gene IDs, SwissProt (SP) IDs, gene names, gene…
Apr 19, 2022
Sam White
 

RNA Isolation - O.nerka Berdahl Brain Tissues

2022
Miscellaneous
Steven asked that I isolate RNA from the remainder of the Berdahl brain tissue samples (GitHub issue).
Apr 11, 2022
Sam White
 

Server Maintenance - Fix Server Certificate Authentication Issues

github
InCommon
certificate
servers
gannet
owl
eagle
2022
Computer Servicing
We had been encountering issues when linking to images in GitHub (e.g. notebooks, Issues/Discussions) hosted on our servers (primarily Gannet). Images always showed up as…
Apr 2, 2022
Sam White
 

Nextflow - Trials and Tribulations of Installing and Using NF-Core RNAseq

2022
Miscellaneous
For some reason, I struggled to get things installed correctly. Installing Nextflow was straightforward and didn’t have any issues. First bump in the road came from the insta…
Mar 25, 2022
Sam White
 

Data Wrangling - P.generosa Genomic Feature FastA Creation

2022
Miscellaneous
Steven wanted me to generate FastA files (GitHub Issue) for Panopea generosa (Pacific geoduck) coding sequences (CDS), genes, and mRNAs. One of the primary needs, though…
Mar 24, 2022
Sam White
 

Differential Gene Expression - P.generosa DGE Between Tissues Using Nextlow NF-Core RNAseq Pipeline on Mox

nextflow
Panopea generosa
Pacific geoduck
RNAseq
nf-core
mox
2022
Miscellaneous
Steven asked that I obtain relative expression values for various geoduck tissues (GitHub Issue). So, I decided to use this as an opportunity to try to use a Nextflow pipelin…
Mar 23, 2022
Sam White
 

Data Analysis - C.virginica BSseq Unmapped Reads Using MEGAN6

2022
Miscellaneous
After performing DIAMOND BLASTx and DAA “meganization” on 20220302, the next step was to import the DAA files into MEGAN6 for analyzing the resulting taxonomic assignments…
Mar 9, 2022
Sam White
 

Data Analysis - C.virginica RNAseq Zymo ZR4059 Analyzed by ZymoResearch

2022
Miscellaneous
After realizing that the Crassostrea virginica (Eastern oyster) RNAseq data had relatively low alignment rates (see this notebook entry from 20220224 for a bit more…
Mar 2, 2022
Sam White
 

Taxonomic Assignment - C.virginica BSseq Unmapped Reads Using DIAMOND BLASTx and MEGAN6 on Mox

2022
Miscellaneous
After mapping bisulfite sequencing (BSseq) data to the Crassostrea virginica (Eastern oyster) genome, Steven noticed that there were a large number of unmapped reads. He…
Mar 2, 2022
Sam White
 

Data Wrangling - P.generosa Genome GFF Conversion to GTF Using gffread

2022
Miscellaneous
Steven asked in this GitHub Issue to convert our Panopea generosa (Pacific geoduck) genomic GFF to a GTF for use in the 10x Genomics Cell Ranger software. This conversion…
Mar 1, 2022
Sam White
 

Transcript Identification and Alignments - C.virginica RNAseq with NCBI Genome GCF_002022765.2 Using Hisat2 and Stringtie on Mox

hisat2
stringtie
Crassostrea virginica
Eastern oyster
RNAseq
GCF_002022765.2
2022
Miscellaneous
After an additional round of trimming yesterday, I needed to identify alternative transcripts in the Crassostrea virginica (Eastern oyster) gonad RNAseq data we have. I…
Feb 25, 2022
Sam White
 

Trimming - Additional 20bp from C.virginica Gonad RNAseq with fastp on Mox

fastp
mox
Crassostrea virginica
RNAseq
trimming
Eastern oyster
2022
Miscellaneous
When I previously aligned trimmed RNAseq reads to the NCBI C.virginica genome (GCF_002022765.2) on 20210726, I specifically noted that alignment rates were consistently…
Feb 24, 2022
Sam White
 

Data Wrangling - C.virginica lncRNA Extractions from NCBI GCF_002022765.2 Using GffRead

2022
Miscellaneous
Continuing to work on our Crassostrea virginica (Eastern oyster) project examining the effects of OA on female and male gonads (GitHub repo), Steven tasked me with parsing…
Feb 17, 2022
Sam White
 

Transcriptome Assembly - Genome-guided C.virginica Adult Gonad OA RNAseq Using Trinity on Mox

2022
Miscellaneous
As part of this project, Steven’s asked that I identify long, non-coding RNAs (lncRNAs) (GitHub Issue) in the Crassostrea virginica (Eastern oyster) adult OA gonad RNAseq…
Feb 7, 2022
Sam White
 

RNAseq Alignment - C.virginica Adult OA Gonad Data to GCF_002022765.2 Genome Using HISAT2 on Mox

HISAT2
Crassostrea virginica
RNAseq
Mox
Eastern oyster
2022
Miscellaneous
As part of this project epigeneticstoocean/2018_L18-adult-methylation (private GitHub repo), Steven’s asked that I identify long, non-coding RNAs (lncRNAs) (GitHub Issue) in…
Jan 31, 2022
Sam White
 

Data Wrangling - C.virginica Gonad RNAseq Transcript Counts Per Gene Per Sample Using Ballgown

data wrangling
Crassostrea virginica
eastern oyster
R
ballgown
2022
Miscellaneous
As we continue to work on the analysis of impacts of OA on Crassostrea virginica (Eastern oyster) gonads via DNA methylation and RNAseq…
Jan 27, 2022
Sam White
 

Data Received - C.virginica OA Larvae DNA Methylation FastQs from Lotterhos Lab

Crassostrea virginica
Eastern oyster
larvae
DNA methylation
data received
2022
Data Received
In this GitHub Issue Steven asked that I download Crassostrea virginica (Eastern oyster) OA larval DNA methylation sequencing data from the Lotterhos Lab. The data is part…
Jan 19, 2022
Sam White
 

Project Summary - Matt George PSMFC Mytilus Byssus Project

2022
Project Summary
This will be a “dynamic” notebook entry, whereby I will update this post continually as I process new samples, analyze new data, etc for this project. The hope is to make it…
Jan 13, 2022
Sam White
 

RNA Isolation - O.nerka Berdahl Brain Tissues

2022
Miscellaneous
The previous round of RNA isolation on 20211222 had poor yields for the brain tissue. As such, I needed to attempt to obtain RNA from some additional brain tissues.
Jan 12, 2022
Sam White
 

RNA Isolation - M.trossulus Gill

2022
Miscellaneous
As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by continuing isolating RNA from a relatively large…
Jan 12, 2022
Sam White
 

RNA Isolation - M.trossulus Gill and Phenol Gland

2022
Miscellaneous
As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by continuing isolating RNA from a relatively large…
Jan 11, 2022
Sam White
 

RNA Isolation - M.trossulus Gill and Phenol Gland

2022
Miscellaneous
As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by continuing isolating RNA from a relatively large…
Jan 10, 2022
Sam White
 

RNA Isolation - M.trossulus Gill and Phenol Gland

2022
Miscellaneous
As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by continuing isolating RNA from a relatively large…
Jan 9, 2022
Sam White
 

RNA Isolation - M.trossulus Phenol Gland and Gill

2021
Miscellaneous
As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by continuing isolating RNA from a relatively large…
Dec 23, 2021
Sam White
 

RNA Isolation - M.trossulus Foot and Phenol Gland

2021
Miscellaneous
As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by isolating RNA from a relatively large number of…
Dec 22, 2021
Sam White
 

Project Summary - O.nerka Berdahl Samples

2021
Project Summary
This will be a “dynamic” notebook entry, whereby I will update this post continually as I process new samples, analyze new data, etc for this project. The hope is to make it…
Dec 22, 2021
Sam White
 

RNA Isolation - O.nerka Berdahl Brain Tissues

2021
Miscellaneous
The previous round of RNA isolation (on 20211220) had poor yields for the brain tissue. As such, I needed to attempt to obtain RNA from some additional brain tissues.
Dec 22, 2021
Sam White
 

RNA Isolation - O.nerka Berdahl Tissues

RNA isolation
qubit
RNA quantification
RNA
2021
Miscellaneous
Finally got around to tackling this GitHub issue regarding isolating RNA from some Oncorhynchus nerka (sockeye salmon) tissues we have from Andrew Berdahl’s lab (a UW SAFS…
Dec 20, 2021
Sam White
 

Data Wrangling - C.virginica NCBI GCF_002022765.2 GFF to Gene BED File

2021
Miscellaneous
When working to identify differentially expressed transcripts (DETs) and genes (DEGs) for our Crassostrea virginica (Eastern oyster) RNAseq/DNA methylation comparison of…
Dec 9, 2021
Sam White

Differential Transcript Expression - C.virginica Gonad RNAseq Using Ballgown

Crassostrea virginica
Eastern oyster
gonad
RNAseq
ballgown
DEG
DET
expression
2021
Miscellaneous
In preparation for differential transcript analysis, I previously ran our RNAseq data through StringTie on 20210726 to identify and quantify transcripts. Identification of…
Oct 21, 2021
Sam White
 

SNP Characterization - C.bairdi v3.1 Transcriptome Assembly and Day2 DEG Pooled Samples RNAseq Data

2021
Tanner Crab RNAseq
I previously identified variants across the four Day 2 DEG pooled RNAseq samples (380822, 380823, 380824, 380825) on 20210909 within the cbai_transcriptome_v3.1 transcriptome…
Oct 5, 2021
Sam White
 

SNP Identification - C.bairdi Day 2 DEG Pooled Samples Using bcftools on Mox

bcftools
Tanner crab
Chionoecetes bairdi
Mox
SNP
2021
Tanner Crab RNAseq
After getting our the RNAseq data aligned with HISAT2 on 20210908, the next step was to make variant calls. I opted to do so using bcftools mpileup. Previously, this was…
Sep 9, 2021
Sam White
 

RNAseq Alignments - C.bairdi Day 2 Infected-Uninfected Temperature Increase-Decrease RNAseq to cbai_transcriptome_v3.1.fasta with Hisat2 on Mox

hisat2
alignment
RNAseq
Tanner crab
Chionoecetes bairdi
mox
2021
Tanner Crab RNAseq
Ealier today, I created the necessary Hisat2 index files for cbai_transcriptome_v3.1. Next, I needed to actually get the alignments run. The alignments were performed using H…
Sep 8, 2021
Sam White
 

Assembly Indexing - C.bairdi Transcriptome cbai_transcriptome_v3.1.fasta with Hisat2 on Mox

2021
Tanner Crab RNAseq
We recently received reviews back for the Tanner crab paper submission (“Characterization of the gene repertoire and environmentally driven expression patterns in Tanner…
Sep 8, 2021
Sam White
 

Computer Servicing - APC SUA2200RM2U UPS Battery Replacement

battery
ups
apc
2021
Computer Servicing
Replaced the battery pack in the top APC SUA2200RM2U UPS in our computing “cluster” cabinet.
Aug 24, 2021
Sam White
 

Computer Management - Disable Sleep and Hibernation on Raven

raven
ubuntu
sleep
2021
Computer Servicing
We’ve been having an issue with our computer Raven where it would become inaccessible after some time after a reboot. Attempts to remote in would just indicate no route to…
Aug 24, 2021
Sam White
 

Uninterruptible Power Supply - Battery Replacement for APS BR1000G

2021
Computer Servicing
Replace battery in uninterruptible power supply APS BR1000G for Owl in FTR 230.
Aug 11, 2021
Sam White
 

Transcript Identification and Quantification - C.virginia RNAseq With NCBI Genome GCF_002022765.2 Using StringTie on Mox

2021
Miscellaneous
After having run HISAT2 to index and identify exons and splice sites in the NCBI Crassostrea virginica (Eastern oyster) genome (GCF_002022765.2) on 20210720, the next step…
Jul 26, 2021
Sam White
 

Genome Annotations - Splice Site and Exon Extractions for C.virginica GCF_002022765.2 Genome Using Hisat2 on Mox

2021
Miscellaneous
Previously performed quality trimming on the Crassostrea virginica (Eastern oyster) gonad/sperm RNAseq data on 20210714. Next, I needed to identify exons and splice sites…
Jul 20, 2021
Sam White
 

Trimming - C.virginica Gonad RNAseq with FastP on Mox

2021
Miscellaneous
Needed to trim the Crassostrea virginica (Eastern oyster) gonad RNAseq data we received on 20210528.
Jul 14, 2021
Sam White
 

Summary - Geoduck RNAseq Data

2021
Project Summary
Per this GitHub Issue, I’ve compiled a summary table, with links, of all of our Panopea generosa (Pacific geoduck) RNAseq data as it exists in NCBI. This will be a “dynamic”…
Jul 12, 2021
Sam White
 

Genome Analysis - Identification of Potential Contaminating Sequences in Panopea-generosa-v1.0 Assembly Using BlobToolKit on Mox

2021
Geoduck Genome Sequencing
As part of our Panopea generosa (Pacific geoduck) genome sequencing efforts, Steven came across a tool designed to help identify if there are any contaminating sequences in…
Jul 12, 2021
Sam White
 

FastQC-MultiQC - Yaamini's C.virginica RNAseq and WGBS from ZymoResearch on Mox

2021
Miscellaneous
Finally got around to running FastQC on Yaamini’s RNAseq and WGBS sequencing data recieved on 20210528.
Jun 29, 2021
Sam White
 

Data Wrangling - S.salar Gene Annotations from NCBI RefSeq GCF_000233375.1_ICSASG_v2_genomic.gff for Shelly

2021
Miscellaneous
Shelly posted a GitHub Issue asking if I could create a file of S.salar genes with their UniProt annotations (e.g. gene name, UniProt accession, GO terms).
Jun 1, 2021
Sam White
 

Data Received - Yaamini's C.virginica WGBS and RNAseq Data from ZymoResearch

2021
Data Received
Yaamini received her sequencing data from ZymoResearch; both whole genome bisfulfite sequencing (WGBS) and RNAseq. I was tasked with downloading the data and running QC.
May 28, 2021
Sam White
 

Assembly Comparisons - Ostrea lurida Non-scaffold Genome Assembly Comparisons Using Quast on Swoose

swoose
quast
Ostrea lurida
Olympia oyster
2021
Olympia Oyster Genome Assembly
After generating a new Ostrea lurida genome assembly (v090) on 20210520, I decided to compare with our previous genome assemblies. Here, I compared v090 with all of our…
May 21, 2021
Sam White
 

Assembly Assessment - Olurida_v090 Using Quast on Swoose

2021
Olympia Oyster Genome Assembly
After running a new Ostrea lurida assembly yesterday (Olurida_v090), I evaluated Olurida_v090 using Quast to produce some stats. This was run on my local computer with the…
May 21, 2021
Sam White
 

Genome Assembly - Olurida_v090 with BGI Illumina and PacBio Hybrid Using Wengan on Mox

2021
Olympia Oyster Genome Assembly
I was recently tasked with adding annotations for our Ostrea lurida genome assembly to NCBI. As it turns out, adding just annotation files can’t be done since the genome was…
May 20, 2021
Sam White
 

Trimming - O.lurida BGI FastQs with FastP on Mox

fastp
mox
Ostrea lurida
Olympia oyster
trimming
2021
Olympia Oyster Genome Sequencing
After attempting to submit our Ostrea lurida (Olympia oyster) genome assembly annotations (via GFF) to NCBI, the submission process also highlighted some short comings of the …
May 18, 2021
Sam White
 

Genome Submission - Validation of Olurida_v081.fa and Annotated GFFs Prior to Submission to NCBI

2021
Olympia Oyster Genome Assembly
Per this GitHub Issue, Steven has asked to get our Ostrea lurida (Olympia oyster) genome assembly (Olurida_v081.fa) submitted to NCBI with annotations. The first step in the…
May 13, 2021
Sam White
 

RepeatMasker - C.gigas Rosling NCBI Genome GCA_902806645.1 on Mox

GCA_902806645.1
mox
repeatmasker
Crassostrea gigas
Pacific oyster
2021
Miscellaneous
Decided to tackle this GitHub Issue about creating a transposable elements IGV track with the new Roslin C.gigas genome, since it had been sitting for a while and I have…
May 4, 2021
Sam White
 

Singularity - RStudio Server Container on Mox

computing
Rstudio Server
mox
singularity
2021
Miscellaneous
Aidan recently needed to use R on a machine with more memory. Additionally, it would be ideal if he could use RStudio. So, I managed to figure out how to set up a…
Apr 23, 2021
Sam White
 

Read Mapping - 10x-Genomics Trimmed FastQ Mapped to P.generosa v1.0 Assembly Using Minimap2 for BlobToolKit on Mox

2021
Miscellaneous
To continue towards getting our Panopea generosa (Pacific geoduck) genome assembly (v1.0) analyzed with BlobToolKit, per this GitHub Issue, I’ve decided to run each aspect…
Apr 15, 2021
Sam White
 

Genome Annotation - P.generosa v1.0 Assembly Using DIAMOND BLASTx for BlobToolKit on Mox

2021
Miscellaneous
To continue towards getting our Panopea generosa (Pacific geoduck) genome assembly (v1.0) analyzed with BlobToolKit, per this GitHub Issue, I’ve decided to run each aspect…
Apr 15, 2021
Sam White
 

Genome Annotation - P.generosa v1.0 Assembly Using BLASTn for BlobToolKit on Mox

2021
Miscellaneous
To continue towards getting our Panopea generosa (Pacific geoduck) genome assembly (v1.0) analyzed with BlobToolKit, per this GitHub Issue, I’ve decided to run each aspect…
Apr 15, 2021
Sam White
 

Trimming P.generosa 10x Genomics HiC FastQs with fastp on Mox

2021
Miscellaneous
Steven asked me to try running Blob Tool Kit to identify potential contaminating sequence in our Panopea generosa (Pacific geoduck) genome assembly (v1.0). In preparation…
Apr 1, 2021
Sam White
 

Transcriptome Annotation - Trinotate on C.bairdi Transcriptome v4.0 on Mox

2021
Miscellaneous
Continued annotation of cbai_transcriptome_v4.0.fasta [Trinity de novo assembly from…
Mar 18, 2021
Sam White
 

Transcriptome Annotation - DIAMOND BLASTx on C.bairdi Transcriptome v4.0 on Mox

2021
Miscellaneous
Continued annotation of cbai_transcriptome_v4.0.fasta [Trinity de novo assembly from…
Mar 18, 2021
Sam White
 

TransDecoder - C.bairdi Transcriptome v4.0 on Mox

2021
Tanner Crab RNAseq
Began annotation of cbai_transcriptome_v4.0.fasta Trinity de novo assembly from 20210317] using TransDecoder on Mox. This will be used as a component of Trinotate annotation…
Mar 17, 2021
Sam White
 

Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v4.0 on Mox

2021
Tanner Crab RNAseq
I previously created a C.bairdi de novo transcriptome assembly v4.0 with Trinity from all our C.bairdi RNAseq reads which had BLASTx matches to the C.opilio genome and…
Mar 17, 2021
Sam White
 

Transcriptome Assembly - C.bairdi Transcriptome v4.0 Using Trinity on Mox

mox
Tanner crab
Chionoecetes bairdi
Trinity
transcriptome
assembly
RNAseq
2021
Tanner Crab RNAseq
Continuing to addressing this GitHub issue, to generate an additional C.bairdi transcriptome, I finally got to the point of actually running the assembly using Trinity using …
Mar 17, 2021
Sam White
 

Read Extractions - C.bairdi RNAseq Reads from C.opilio BLASTx Matches with seqkit on Mox

2021
Tanner Crab RNAseq
As part of addressing this GitHub issue, to generate an additional C.bairdi transcriptome, I needed to extract the reads ID’ed via BLASTX against the C.opilio genome on…
Mar 16, 2021
Sam White
 

DIAMOND BLASTx - C.bairdi RNAseq vs C.opilio Genome Proteins on Mox

2021
Tanner Crab RNAseq
We want to generate an additional Tanner crab (Chionoecetes bairdi) transcriptome, per this GitHub issue, to generate an additional C.bairdi transcriptome. This has come…
Mar 12, 2021
Sam White
 

Transcriptome Annotation - Trinotate Hematodinium v1.7 on Mox

2021
Miscellaneous
To continue annotation of our Hematodinium v1.7 transcriptome assembly, I wanted to run Trinotate.
Mar 9, 2021
Sam White
 

Transcriptome Annotation - Trinotate Hematodinium v1.6 on Mox

2021
Miscellaneous
To continue annotation of our Hematodinium v1.6 transcriptome assembly, I wanted to run Trinotate.
Mar 9, 2021
Sam White
 

Transcriptome Assembly - Hematodinium Transcriptomes v1.6 and v1.7 with Trinity on Mox

Tanner crab
hematodinium
mox
trinity
Chionoecetes bairdi
2021
Miscellaneous
I’d previously assembled hemat_transcriptome_v1.0.fasta on 20200122, hemat_transcriptome_v1.5.fasta on 20200408, extracted hemat_transcriptome_v2.1.fasta from an existing…
Mar 8, 2021
Sam White
 

Data Wrangling - Gene ID Extraction from P.generosa Genome GFF Using Methylation Machinery Gene IDs

2021
Miscellaneous
Per this GitHub issue, Steven provided a list of methylation-related gene names and wanted to extract the corresponding Panopea generosa ([Pacific geoduck (Panopea generosa)]…
Feb 26, 2021
Sam White
 

Data Wrangling - Gene ID Extraction from P.generosa Genome GFF Using Methylation Machinery List

2021
Miscellaneous
Per this GitHub Issue Steven asked that I take a list of gene names associated with DNA methylation and see if I could extract a list of Panopea generosa (Panopea generosa) g…
Feb 26, 2021
Sam White
 

SRA Submission - A.elegantissima ONT Fast5 from Jay Dimond

2021
SRA Submission
At the beginning of the month, Jay sent us his A.elegantissima ONT Fast5 data in order to help him get it submitted to NCBI Sequencing Read Archive (SRA).
Feb 9, 2021
Sam White
 

Data Received - Anthopleura elegantissima - aggregating anenome - NanoPore Genome Sequence from Jay Dimond

2021
Miscellaneous
Jay asked me to help get his A.elegantissima (aggregating anenome) NanoPore gDNA sequencing data submitted to NCBI Sequencing Read Archive (SRA). He sent a hard drive (HDD)…
Feb 1, 2021
Sam White
 

Samples Submitted - M.magister MBD-BSseq Libraries to Univ. of Oregon GC3F

Metacarcinus magister
sequencing
Dungeness crab
Cancer magister
2021
Miscellaneous
Submitted the M.magister MBD-BSseq libraries created 20201124 using the 4nM aliquots created for the MiSeq test run on 20201202 to the Univ. of Oregon GC3F sequencing core.
Jan 12, 2021
Sam White
 

Transcriptome Comparisons - C.bairdi Transcriptomes Evaluations with DETONATE rsem-eval on Mox

2020
Tanner Crab RNAseq
UPDATE: I’ll lead in with the fact that this failed with an error message that I can’t figure out. This will save the reader some time. I’ve posted the problem as an Issue…
Dec 29, 2020
Sam White
 

Alignments - C.bairdi RNAseq Transcriptome Alignments Using Bowtie2 on Mox

2020
Tanner Crab RNAseq
I had previously attempted to compare all of our C.bairdi transcriptome assemblies using DETONATE on 20200601, but, due to hitting time limits on Mox, failed to successfully…
Dec 24, 2020
Sam White
 

Samples Received - Cockle Clam Gonad H and E Slides

2020
Samples Received
Today we received the H & E-stained slides from the cockle clam gonad tissue blocks/cassettes we submitted on 20201201. Slides were added to Slide Case #5 - Rows 13 - 37 (Goo…
Dec 17, 2020
Sam White
 

FastQC-MultiQC - M.magister MBD-BSseq Pool Test MiSeq Run on Mox

2020
Miscellaneous
Earlier today we received the M.magister (C.magister; Dungeness crab) MiSeq data from Mac.
Dec 11, 2020
Sam White
 

Data Received - M.magister MBD-BSseq Pool Test MiSeq Run

2020
Miscellaneous
After creating _M.magister (C.magister; Dungeness crab) MBD-BSseq libraries (on 20201124), I gave the pooled set of samples to Mac for a test sequencing run on the MiSeq on…
Dec 11, 2020
Sam White
 

Alignment - C.gigas RNAseq to GCF_000297895.1_oyster_v9 Genome Using STAR on Mox

2020
Miscellaneous
Mac was getting some weird results when mapping some single cell RNAseq data to the C.gigas mitochondrial (mt) genome that she had, so she asked for some help mapping other C…
Dec 8, 2020
Sam White
 

SRA Submission - Haws Lab C.gigas Ploidy pH WGBS

2020
SRA Submission
I submitted the 24 C.gigas diploid/triploid pH-treated WGBS sequence data we received 20201205 to the NCBI Sequence Read Archive (SRA).
Dec 7, 2020
Sam White
 

Trimming - Haws Lab C.gigas Ploidy pH WGBS 10bp 5 and 3 Prime Ends Using fastp and MultiQC on Mox

2020
Miscellaneous
Making the assumption that the 24 C.gigas ploidy pH WGBS data we receved 20201205 will be analyzed using Bismark, I decided to go ahead and trim the files according to Bismark…
Dec 6, 2020
Sam White
 

FastQC-MultiQc - C.gigas Ploidy pH WGBS Raw Sequence Data from Haws Lab on Mox

2020
Miscellaneous
[Yesterday (20201205), we received the whole genome bisulfite sequencing (WGBS) data back from…
Dec 6, 2020
Sam White
 

Data Received - C.gigas Diploid-Triploid pH Treatments Ctenidia WGBS from ZymoResearch

2020
Data Received
Today we received the whole genome bisulfite sequencing (WGBS) from the 24 C.gigas diploid-triploid samples subjected to different pH that were submitted 20200824. The…
Dec 5, 2020
Sam White
 

Trimming - Ronits C.gigas Ploidy WGBS 10bp 5 and 3 Prime Ends Using fastp and MultiQC on Mox

2020
Miscellaneous
Steven asked me to trim (GitHub Issue) Ronit’s WGBS sequencing data we received on 20201110, according to Bismark guidelines for libraries made with the ZymoResearch Pico…
Dec 2, 2020
Sam White
 

Sample Submission - M.magister MBD BSseq Libraries for MiSeq at NOAA

2020
Samples Submitted
Earlier today I quantified the libraries with the Qubit in preparation for sample pooling and sequencing. Before performing a full sequencing run, Mac wanted to select a…
Dec 2, 2020
Sam White
 

Library Quantification - M.magister MBD BSseq Libraries with Qubit

2020
Miscellaneous
After reviewing the Bionalyzer assays for the MBD BSseq libraries Mac indicated she’d like to have the libraries quantified using the Qubit.
Dec 2, 2020
Sam White
 

Samples Submitted - Cockle Clam Gonad Histology Cassettes for H and E

2020
Samples Submitted
Per this GitHub Issue, Steven asked that I submit a set of fixed cockle clam gonad tissues (currently stored in histology cassettes in 70% EtOH) for Hematoxylin and eosin…
Dec 1, 2020
Sam White
 

Trimming - Ronits C.gigas Ploidy WGBS Using fastp and MultiQC on Mox

2020
Miscellaneous
Steven asked me to trim (GitHub Issue) Ronit’s WGBS sequencing data we received on 20201110, according to Bismark guidelines for libraries made with the ZymoResearch Pico…
Nov 30, 2020
Sam White
 

Bioanalyzer - M.magister MBD BSseq Libraries

2020
Miscellaneous
MBD BSseq library construction was completed yesterday (20201124). Next, I needed to evaluate the libraries using the Roberts Lab Bioanalyzer 2100 (Agilent) to assess…
Nov 25, 2020
Sam White
 

MBD BSseq Library Prep - M.magister MBD-selected DNA Using Pico Methyl-Seq Kit

2020
Miscellaneous
After finishing the final set of eight MBD selections on 20201103, I’m finally ready to make the BSseq libraries using the Pico Methyl-Seq Library Prep Kit (ZymoResearch) (PD…
Nov 24, 2020
Sam White
 

RNA Isolation and Quantification - P.generosa Hemocytes from Shelly

2020
Miscellaneous
Shelly asked me to isolate RNA from some P.generosa hemocytes (GitHub Issue) that she had.
Nov 19, 2020
Sam White
 

SRA Submission - Ronits C.gigas Ploidy WGBS

2020
SRA Submission
A few days ago, we received the whole genome bisulfite sequencing (WBGS) data (20201110) from Ronit’s C.gigas diploid/triploid dessication/heat stress experiment (GitHub repo)…
Nov 13, 2020
Sam White
 

FastQC-MultiQc - C.gigas Ploidy WGBS Raw Sequence Data from Ronits Project on Mox

2020
Miscellaneous
Earlier today, we received the C.gigas ploidy WGBS data that we submitted to ZymoResearch on 20200820.
Nov 10, 2020
Sam White
 

Transcriptome Assessment - Crustacean Transcripome Completeness Evaluation Using BUSCO on Mox

2020
Miscellaneous
Grace was recently working on writing up a manuscript which did a basic comparison of our C.bairdi transcriptome (cbai_transcriptome_v3.1) (see the Genomic Resources wiki for…
Nov 10, 2020
Sam White
 

Data Received - C.gigas Ploidy WGBS from Ronits Project via ZymoResearch

2020
Data Received
We received the data from our whole genome bisulfite sequencing (WGBS) submission to ZymoResearch on 2020820 for Ronit’s C.gigas diploid/triploid dessication/heat stress…
Nov 10, 2020
Sam White
 

Data Wrangling - MultiQC on S.salar RNAseq from fastp and HISAT2 on Mox

2020
Miscellaneous
In Shelly’s GitHub Issue for this S.salar project, she also requested a MultiQC report for the trimming (completed on 20201029) and the genome alignments (completed on…
Nov 6, 2020
Sam White
 

Hard Drive Upgrade - Gannet Synology Server

2020
Computer Servicing
Completed upgrading the 12 x 8TB HDDs in our server, Gannet (Synology RS3618XS), to 12 x 16TB HDDs. The process was simple, but the repair process took ~20hrs for each new…
Nov 5, 2020
Sam White
 

RNAseq Alignments - S.salar HISAT2 BAMs to GCF_000233375.1_ICSASG_v2_genomic.gtf Transcriptome Using StringTie on Mox

2020
Miscellaneous
This is a continuation of addressing Shelly Trigg’s (regarding some Salmo salar RNAseq data) request (GitHub Issue) to trim (completed 20201029), perform genome alignment (co…
Nov 4, 2020
Sam White
 

RNAseq Alignments - Trimmed S.salar RNAseq to GCF_000233375.1_ICSASG_v2_genomic.fa Using Hisat2 on Mox

2020
Miscellaneous
This is a continuation of addressing Shelly Trigg’s (regarding some Salmo salar RNAseq data) request (GitHub Issue) to trim (completed 20201029), perform genome alignment…
Nov 3, 2020
Sam White
 

MBD Selection - M.magister Sheared Gill gDNA 16 of 24 Samples Set 3 of 3

2020
Miscellaneous
Click here for notebook on the first eight samples processed. Click here for the second set of eight samples processed. M.magister (Dungeness crab) gill gDNA provided by…
Nov 3, 2020
Sam White
 

MBD Selection - M.magister Sheared Gill gDNA 8 of 24 Samples Set 2 of 3

2020
Miscellaneous
Click here for notebook on the first eight samples processed. M.magister (Dungeness crab) gill gDNA provided by Mackenzie Gavery was previously sheared on 20201026 and three…
Nov 2, 2020
Sam White
 

Trimming - Shelly S.salar RNAseq Using fastp and MultiQC on Mox

2020
Miscellaneous
Shelly asked that I trim, align to a genome, and perform transcriptome alignment counts in this GitHub issue with some Salmo salar RNAseq data she had and, using a subset of…
Oct 29, 2020
Sam White
 

MBD Selection - M.magister Sheared Gill gDNA 8 of 24 Samples Set 1 of 3

2020
Miscellaneous
M.magister (Dungeness crab) gill gDNA provided by Mackenzie Gavery was previously sheared on 20201026 and three samples were subjected to additional rounds of shearing on 202…
Oct 28, 2020
Sam White
 

DNA Shearing - M.magister gDNA Additional Shearing CH05-01_21 CH07-11 and Bioanalyzer

2020
Miscellaneous
After shearing all of the M.magister gill gDNA on 20201026, there were still three samples that still had average fragment lengths that were a bit longer than desired…
Oct 27, 2020
Sam White
 

DNA Shearing - M.magister gDNA Shearing All Samples and Bioanalyzer

2020
Miscellaneous
I previously ran some shearing tests on 20201022 to determine how many cycles to run on the sonicator (Bioruptor 300; Diagenode) to achieve an average fragment length of…
Oct 26, 2020
Sam White
 

DNA Shearing - M.magister CH05-21 gDNA Full Shearing Test and Bioanalyzer

2020
Miscellaneous
Yesterday, I did some shearing of Metacarcinus magister gill gDNA on a test sample (CH05-21) to determine how many cycles to run on the sonicator (Bioruptor 300; Diagenode)…
Oct 22, 2020
Sam White
 

DNA Shearing - M.magister gDNA Shear Testing and Bioanalyzer

2020
Miscellaneous
Steven assigned me to do some MBD-BSseq library prep (GitHub Issue) for some Dungeness crab (Metacarcinus magister) DNA samples provided by Mackenzie Gavery. The DNA was…
Oct 21, 2020
Sam White
 

Read Mapping - C.bairdi 201002558-2729-Q7 and 6129-403-26-Q7 Taxa-Specific NanoPore Reads to cbai_genome_v1.01.fasta Using Minimap2 on Mox

2020
Miscellaneous
After extracting FastQ reads using seqtk on 20201013 from the various taxa I had been interested in, the next thing needed doing was mapping reads to the cbai_genome_v1.01 “g…
Oct 14, 2020
Sam White
 

Data Wrangling - C.bairdi NanoPore Reads Extractions With Seqtk on Mephisto

2020
Miscellaneous
In my pursuit to identify which contigs/scaffolds of our “C.bairdi” genome assembly from 20200917 correspond to interesting taxa, based on taxonomic assignments produced by…
Oct 13, 2020
Sam White
 

NanoPore Reads Extractions - C.bairdi Taxonomic Reads Extractions with MEGAN6 on 201002558-2729-Q7 and 6129-403-26-Q7

2020
Miscellaneous
After completing the taxonomic comparisons of 201002558-2729-Q7 and 6129-403-26-Q7 on 20201002, I decided to extract reads assigned to the following taxa for further…
Oct 7, 2020
Sam White
 

Comparison - C.bairdi 20102558-2729 vs. 6129-403-26 NanoPore Taxonomic Assignments Using MEGAN6

2020
Miscellaneous
After noticing that the initial MEGAN6 taxonomic assignments for our combined C.bairdi NanoPore data from 20200917 revealed a high number of bases assigned to E.canceri and A…
Oct 2, 2020
Sam White
 

Taxonomic Assignments - C.bairdi 6129-403-26-Q7 NanoPore Reads Using DIAMOND BLASTx on Mox and MEGAN6 daa2rma on emu

2020
Miscellaneous
After noticing that the initial MEGAN6 taxonomic assignments for our combined C.bairdi NanoPore data from 20200917 revealed a high number of bases assigned to E.canceri and A…
Sep 28, 2020
Sam White
 

Taxonomic Assignments - C.bairdi 20102558-2729-Q7 NanoPore Reads Using DIAMOND BLASTx on Mox and MEGAN6 daa2rma on emu

2020
Miscellaneous
After noticing that the initial MEGAN6 taxonomic assignments for our combined C.bairdi NanoPore data from 20200917 revealed a high number of bases assigned to E.canceri and A…
Sep 28, 2020
Sam White
 

Data Wrangling - C.bairdi NanoPore 6129-403-26 Quality Filtering Using NanoFilt on Mox

2020
Miscellaneous
Last week, I ran all of our Q7-filtered C.baird NanoPore reads through MEGAN6 to evaluate the taxonomic breakdown (on 20200917) and noticed that there were a large quantity…
Sep 28, 2020
Sam White
 

Data Wrangling - C.bairdi NanoPore 20102558-2729 Quality Filtering Using NanoFilt on Mox

2020
Miscellaneous
Last week, I ran all of our Q7-filtered C.baird NanoPore reads through MEGAN6 to evaluate the taxonomic breakdown (on 20200917) and noticed that there were a large quantity…
Sep 28, 2020
Sam White
 

Assembly Assessment - BUSCO C.bairdi Genome v1.01 on Mox

2020
Miscellaneous
After creating a subset of the cbai_genome_v1.0 of contigs >100bp yesterday (subset named cbai_genome_v1.01), I wanted to generate BUSCO scores for cbai_genome_v1.01. This…
Sep 24, 2020
Sam White
 

Data Wrangling - Subsetting cbai_genome_v1.0 Assembly with faidx

2020
Miscellaneous
Previously assembled cbai_genome_v1.0.fasta with our NanoPore Q7 reads on 20200917 and noticed that there were numerous sequences that were well shorter than the expected…
Sep 23, 2020
Sam White
 

SRA Submissions - NanoPore C.bairdi 20102558-2729 and 6129_403_26

2020
SRA Submission
Submitted our C.bairdi NanoPore sequencing data from 20200109 (Sample 20102558-2729 - uninfected EtOH-preserved muscle) and from 20200311 (Sample 6129_403_26 -…
Sep 21, 2020
Sam White
 

Assembly Assessment - BUSCO C.bairdi Genome v1.0 on Mox

2020
Miscellaneous
After using Flye to perform a de novo assembly of our Q7 filtered NanoPore sequencing data on 20200917, I decided to check the “completeness” of the assembly using BUSCO on…
Sep 18, 2020
Sam White
 

Data Wrangling - C.bairdi NanoPore Quality Filtering Using NanoFilt on Mox

2020
Miscellaneous
I previously converting our C.bairdi NanoPre sequencing data from the raw Fast5 format to FastQ format for our three sets of data:
Sep 17, 2020
Sam White
 

Genome Assembly - C.bairdi - cbai_v1.0 - Using All NanoPore Data With Flye on Mox

2020
Genome Assembly
After quality filtering the C.bairdi NanoPore data earlier today, I performed a de novo assembly using Flye on Mox.
Sep 17, 2020
Sam White
 

Taxonomic Assignments - C.bairdi NanoPore Reads Using DIAMOND BLASTx on Mox and MEGAN6 daa2rma on swoose

2020
Miscellaneous
Earlier today I quality filtered (>=Q7) our C.baird NanoPore reads. One of the things I’d like to do now is to attempt to filter reads taxonomically, since the NanoPore data…
Sep 17, 2020
Sam White
 

qPCR - Geoduck Normalizing Gene Primers 28s-v4 and EF1a-v1 Tests

2020
Miscellaneous
On Monday (20200914), I checked a set of 28s and EF1a primer sets and determined that 28s-v4 and EF1a-v1 were probably the best of the bunch, although they all looked great.…
Sep 16, 2020
Sam White
 

qPCR - Geoduck Normalizing Gene Primer Checks

2020
Miscellaneous
Shelly ordered some new primers (designed by Sam Gurr) (GitHub Issue) to potentially use as normalizing genes for her geoduck reproduction gene expression project and asked…
Sep 14, 2020
Sam White
 

Data Wrangling - Visualization of C.bairdi NanoPore Sequencing Using NanoPlot on Mox

2020
Miscellaneous
I previously converting our C.bairdi NanoPre sequencing data from the raw Fast5 format to FastQ format for our three sets of data:
Sep 14, 2020
Sam White
 

Data Wrangling - NanoPore Fast5 Conversion to FastQ of C.bairdi 6129_403_26 on Mox with GPU Node

2020
Miscellaneous
Time to start working with the NanoPore data that I generated back in March (???!!!). In order to proceed, I first need to convert the raw Fast5 files to FastQ. To do so…
Sep 4, 2020
Sam White
 

Data Wrangling - NanoPore Fast5 Conversion to FastQ of C.bairdi 20102558-2729 Run-02 on Mox with GPU Node

2020
Miscellaneous
Continuing to work with the NanoPore data that I generated back in January(???!!!). In order to proceed, I first need to convert the raw Fast5 files to FastQ. To do so, I’ll…
Sep 4, 2020
Sam White
 

Data Wrangling - NanoPore Fast5 Conversion to FastQ of C.bairdi 20102558-2729 Run-01 on Mox with GPU Node

2020
Miscellaneous
Time to start working with the NanoPore data that I generated back in January(???!!!). In order to proceed, I first need to convert the raw Fast5 files to FastQ. To do so…
Sep 4, 2020
Sam White
 

Samples Submission - Supplemental Ronits C.gigas Diploid-Triploid Ctendidia gDNA for WGBS by ZymoResearch

2020
Samples Submitted
I re-quantified samples for Zymo whole genome bisulfite sequencing (WGBS) project 3534 earlier today due to ZymoResearch indicating there was insufficient DNA for most of…
Sep 1, 2020
Sam White
 

DNA Quantification - Re-quant Ronits C.gigas Diploid-Triploid Ctenidia gDNA Submitted to ZymoResearch

2020
Miscellaneous
I received notice from ZymoResearch yesterday afternoon that the DNA we sent on 20200820 for this project (Quote 3534) had insufficient DNA for sequencing for most of the…
Sep 1, 2020
Sam White
 

Transcriptome Annotation - Trinotate C.bairdi v2.1 on Mox

2020
Tanner Crab RNAseq
To continue annotation of our C.bairdi v2.1 transcriptome assembly], I wanted to run Trinotate.
Aug 31, 2020
Sam White
 

Transcriptome Annotation - Trinotate C.bairdi v3.1 on Mox

2020
Tanner Crab RNAseq
To continue annotation of our C.bairdi v3.1 transcriptome assembly], I wanted to run Trinotate.
Aug 28, 2020
Sam White
 

Transcriptome Annotation - Trinotate Hematodinium v3.1 on Mox

2020
Miscellaneous
To continue annotation of our Hematodinium v3.1 transcriptome assembly, I wanted to run Trinotate.
Aug 26, 2020
Sam White
 

Transcriptome Annotation - Trinotate Hematodinium v2.1 on Mox

2020
Miscellaneous
To continue annotation of our Hematodinium v1.6 transcriptome assembly, I wanted to run Trinotate.
Aug 26, 2020
Sam White
 

TransDecoder - C.bairdi Transcriptomes v2.1 and v3.1 on Mox

2020
Tanner Crab RNAseq
To continue annotation of our C.bairdi v2.1 & v3.1 transcriptome assemblies, I needed to run TransDecoder before performing the more thorough annotation with Trinotate.
Aug 26, 2020
Sam White
 

qPCR - P.generosa RPL5 and TIF3s6b v2 and v3 Normalizing Gene Assessment

2020
Miscellaneous
After testing out the RPL5 and TIF3s6b v2 and v3 primers yesterday on pooled cDNA, we determined the primers looked good, so will go forward testing them on a set of P.genero…
Aug 25, 2020
Sam White
 

Sample Submitted - C.gigas Diploid-Triploid pH Treatments Ctenidia to ZymoResearch for WGBS

2020
Miscellaneous
Submitted 1.5ug of the 24 C.gigas ctenidia ctenidia gDNA isolated last week (20200821) to ZymoResearch for whole genome bisulfite sequencing (WGBS) to compare differences in…
Aug 24, 2020
Sam White
 

qPCR - P.generosa RPL5-v2-v3 and TIF3s6b-v2-v3 Primer Tests

2020
Miscellaneous
Shelly ordered some new primers as potential normalizing genes and asked me to test them out (GitHub Issue).
Aug 24, 2020
Sam White
 

DNA Isolation and Quantification - C.gigas High-Low pH Triploid and Diploid Ctenidia

2020
Miscellaneous
Isolated DNA from 24 of the Crassostrea gigas high/low pH triploid/diploid ctenidia samples that we received yesterday from the Haws Lab. Samples selected by Steven.
Aug 21, 2020
Sam White
 

Samples Received - C.gigas High-Low pH Triploid Diploid from Maria Haws Lab

2020
Samples Received
Received Crassostrea gigas tissue samples from Maria Haws’ Lab at the University of Hawaii Hilo. Tissue samples are a set of triploid and diploid subjected to different pHs.…
Aug 20, 2020
Sam White
 

Samples Submitted - Ronits C.gigas Diploid and Triploid Ctenidia to ZymoResearch for WGBS

2020
Miscellaneous
Submitted 1.75ug of gDNA from 10 Crassostrea gigas ctenidia samples from Ronit’s dessication/temp/ploidy experiment to ZymoResearch for whole genome bisulfite sequencing…
Aug 20, 2020
Sam White
 

Assembly Stats - C.bairdi Transcriptomes v2.1 and v3.1 Trinity Stats on Mox

2020
Miscellaneous
Realized that transcriptomes v2.1 and v3.1 (extracted from BLASTx-annotated FastAs from 20200605) didn’t have any associated stats.
Aug 19, 2020
Sam White
 

Trimming-FastQC-MultiQC - Robertos C.gigas WGBS FastQ Data with fastp FastQC and MultiQC on Mox

2020
Miscellaneous
Steven asked me to trim Roberto’s C.gigas whole genome bisulfite sequencing (WGBS) reads (GitHub Issue) “following his methods”. The only thing specified is trimming…
Aug 18, 2020
Sam White
 

TransDecoder - Hematodinium Transcriptomes v1.6, v1.7, v2.1 and v3.1 on Mox

2020
Miscellaneous
To continue annotation of our Hematodinium v1.6, v1.7, v2.1 & v3.1 transcriptome assemblies, I needed to run TransDecoder before performing the more thorough annotation with …
Aug 17, 2020
Sam White
 

Assembly Stats - cbaiodinium Transcriptomes v2.1 and v3.1 Trinity Stats on Mox

2020
Miscellaneous
Working on dealing with our various cbaiodinium sp. transcriptomes and realized that transcriptomes v2.1 and v3.1 (extracted from BLASTx-annotated FastAs from 20200605)…
Aug 17, 2020
Sam White
 

Transcriptome Assessment - BUSCO Metazoa on Hematodinium v1.6 v1.7 v2.1 and v3.1 on Mox

2020
Miscellaneous
Needed to assess the Hematodinium sp. transcriptomes that I’ve assembled to determine their “completeness” using BUSCO.
Aug 14, 2020
Sam White
 

Transcriptome Annotation - Hematodinium Transcriptomes v1.6 v1.7 v2.1 v3.1 with DIAMOND BLASTx on Mox

2020
Miscellaneous
Needed to annotate the Hematodinium sp. transcriptomes that I’ve assembled using DIAMOND BLASTx. This will also be used for additional downstream annotation (TransDecoder…
Aug 14, 2020
Sam White
 

qPCR - P.generosa APLP and TIF3s8-1 with cDNA

2020
Miscellaneous
Shelly asked me to run some qPCRs (GitHub Issue), after some of the qPCR results I got from primer tests with normalzing genes and potential gene targets.
Aug 6, 2020
Sam White
 

FastQ Read Alignment and Quantification - P.generosa Water Metagenomic Libraries to MetaGeneMark Assembly with Hisat2 on Mox

2020
Miscellaneous
Continuing working on the manuscript for this data, Emma wanted the number of reads aligned to each gene. I previously created and assembly with genes/proteins using…
Jul 31, 2020
Sam White
 

Primer Design and In-Silico Testing - Geoduck Reproduction Primers

2020
Miscellaneous
Shelly asked that I re-run the primer design pipeline that Kaitlyn had previously run to design a set of reproduction-related qPCR primers. Unfortunately, Kaitlyn’s Jupyter…
Jul 30, 2020
Sam White
 

qPCR - Testing P.generosa Reproduction-related Primers

2020
Miscellaneous
Ran some qPCRs on some other primers on 20200723 and then Shelly has asked me to test some additional qPCR primers that might have acceptable melt curves and be usable as…
Jul 29, 2020
Sam White
 

SRA Submission - P.generosa Metagenomics Data

2020
Miscellaneous
Added our P.generosa metagenomics sequencing data to NCBI sequencing read archive (SRA).
Jul 27, 2020
Sam White
 

qPCR - Testing P.generosa Reproduction-related Primers

2020
Miscellaneous
Shelly has asked me to test some qPCR primers related to geoduck reproduction.
Jul 23, 2020
Sam White
 

DNA Isolation and Quantification - C.gigas Diploid (Ronit) and Triploid (Nisbet)

2020
Miscellaneous
Isolated some gDNA from the triploid Nisbet oysters we received on 20200218 and one of Ronit’s diploid ctenidia samples (Google Sheet) using the E.Z.N.A. Mollusc DNA Kit…
Jul 22, 2020
Sam White
 

SRA Submission - Geoduck Epigenetic Ocean Acidification RNAseq

2020
SRA Submission
Can’t remember where it was discussed (probably lab meeting), but I created a GitHub Issue to add all of geoduck RNAseq data to NCBI Short Read Archive (SRA). Anyway, got…
Jul 9, 2020
Sam White
 

ENA Submission - Ostrea lurida draft genome Olurida_v081.fa

2020
Olympia Oyster Genome Sequencing
Submitted our Ostrea lurida v081 genome assembly FastA to the European Nucloetide Archive.
Jul 8, 2020
Sam White
 

Metagenomics - Data Extractions Using MEGAN6

2020
Miscellaneous
Decided to finally take the time to methodically extract data from our metagenomics project so that I have the tables handy when I need them and I can easily share them with…
Jun 18, 2020
Sam White
 

Transcriptome Annotation - C.bairdi Transcriptomes v2.1 and v3.1 Using DIAMOND BLASTx on Mox

2020
Miscellaneous
Decided to annotate the two C.bairdi transcriptomes , cbai_transcriptome_v2.1 and cbai_transcriptome_v3.1, generated on 20200605 using DIAMOND BLASTx on Mox.
Jun 8, 2020
Sam White
 

Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v3.1

2020
Miscellaneous
Continuing to try to identify the best C.bairdi transcriptome, we decided to extract all non-dinoflagellate sequences from cbai_transcriptome_v2.0 (RNAseq shorthand: 2018…
Jun 5, 2020
Sam White
 

Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v2.1

2020
Miscellaneous
Continuing to try to identify the best C.bairdi transcriptome, we decided to extract all non-dinoflagellate sequences from cbai_transcriptome_v2.0 (RNAseq shorthand: 2018…
Jun 5, 2020
Sam White
 

Sequence Extractions - C.bairdi Transcriptomes v2.0 and v3.0 Excluding Alveolata with MEGAN6 on Swoose

2020
Miscellaneous
Continuing to try to identify the best C.bairdi transcriptome, we decided to extract all non-dinoflagellate sequences from cbai_transcriptome_v2.0 (RNAseq shorthand: 2018…
Jun 5, 2020
Sam White
 

Transcriptome Annotation - C.bairdi Transcriptomes v2.0 and v3.0 with DIAMOND BLASTx on Mox

2020
Miscellaneous
Continuing to try to identify the best C.bairdi transcriptome, we decided to extract all non-dinoflagellate sequences from cbai_transcriptome_v2.0 (RNAseq shorthand: 2018…
Jun 4, 2020
Sam White
 

Transcriptome Comparison - C.bairdi Transcriptomes Evaluations with DETONATE on Mox

2020
Miscellaneous
Attempting to get some other metrics regarding our various C.bairdi transcriptome assemblies other than BUSCO scores, I decided to try running DETONATE, as this is a…
Jun 1, 2020
Sam White
 

Transcriptome Comparison - C.bairdi Transcriptomes Compared with DETONATE on Mox

2020
Miscellaneous
We’ve produced a number of C.bairdi transcriptomes and we’re interested in doing some comparisons to try to determine which one might be “best”. I previously compared the…
May 29, 2020
Sam White
 

Transcriptome Annotation - Trinotate C.bairdi Transcriptome-v1.7 on Mox

2020
Miscellaneous
After creating a de novo assembly of C.bairdi transcriptome v1.7 on 20200527, performing BLASTx annotation on 202000527, and TransDecoder for ORF identification on 20200527…
May 29, 2020
Sam White
 

Transcriptome Comparisons - C.bairdi BUSCO Scores

2020
Miscellaneous
Since we’ve generated a number of versions of the C.bairdi transcriptome, we’ve decided to compare them using various metrics. Here, I’ve compared the BUSCO scores generated…
May 28, 2020
Sam White
 

TransDecoder - C.bairdi Transcriptome v1.7 on Mox

2020
Miscellaneous
Need to run TransDecoder on Mox on the C.bairdi transcriptome v1.7 from 20200527.
May 27, 2020
Sam White
 

Transcriptome Annotation - C.bairdi Transcriptome v1.7 Using DIAMOND BLASTx on Mox

2020
Miscellaneous
As part of annotating cbai_transcriptome_v1.7.fasta from 20200527, I need to run DIAMOND BLASTx to use with Trinotate.
May 27, 2020
Sam White
 

Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v1.7

2020
Miscellaneous
I previously created a C.bairdi de novo transcriptome assembly v1.7 with Trinity from all our C.bairdi taxonomically filtered pooled RNAseq samples on 20200527 and decided…
May 27, 2020
Sam White
 

Transcriptome Assembly - C.bairdi All Pooled Arthropoda-only RNAseq Data with Trinity on Mox

2020
Miscellaneous
For completeness sake, I wanted to create an additional C.bairdi transcriptome assembly that consisted of Arthropoda only sequences from just pooled RNAseq data (since I rece…
May 27, 2020
Sam White
 

Transcriptome Annotation - Trinotate C.bairdi Transcriptome-v3.0 on Mox

2020
Miscellaneous
After performing de novo assembly on all of our Tanner crab RNAseq data (no taxonomic filter applied, either) on 20200518, I continued the annotation process by running Trino…
May 26, 2020
Sam White
 

Transcriptome Assembly - P.trituberculatus (Japanese blue crab) NCBI SRA BioProject PRJNA597187 Data with Trinity on Mox

2020
Miscellaneous
After generating a number of C.bairdi (Tanner crab) transcriptomes, we decided we should compare them to evaluate which to help decide which one should become our…
May 23, 2020
Sam White
 

SRA Library Assessment - Determine RNAseq Library Strandedness from P.trituberculatus SRA BioProject PRJNA597187

2020
Miscellaneous
We’ve produced a number of C.bairid transcriptomes utilizing different assembly approaches (e.g. Arthropoda reads only, stranded libraries only, mixed strandedness…
May 21, 2020
Sam White
 

Tutorial - SRA Toolkit for Data Retrieval and Conversion to FastQ

2020
Tutorials
I was looking for some crab transcriptomic data today and, unable to find any previously assembled transcriptomes, turned to the good ol’ NCBI SRA. In order to simplify…
May 21, 2020
Sam White
 

Transcriptome Annotation - Trinotate C.bairdi Transcriptome-v1.6 on Mox

2020
Miscellaneous
After creating a de novo assembly of C.bairdi transcriptome v1.6 on 20200518, performing BLASTx annotation on 202000519, and TransDecoder for ORF identification on 20200519…
May 20, 2020
Sam White
 

TransDecoder - C.bairdi Transcriptome v1.6 on Mox

2020
Miscellaneous
Need to run TransDecoder on Mox on the C.bairdi transcriptome v1.6 from 20200518.
May 19, 2020
Sam White
 

TransDecoder - C.bairdi Transcriptome v3.0 from 20200518 on Mox

2020
Miscellaneous
Need to run TransDecoder on Mox on the C.bairdi transcriptome v3.0 from 20200518.
May 19, 2020
Sam White
 

Transcriptome Annotation - C.bairdi Transcriptome v1.6 Using DIAMOND BLASTx on Mox

2020
Miscellaneous
As part of annotating cbai_transcriptome_v1.6.fasta from 20200518, I need to run DIAMOND BLASTx to use with Trinotate.
May 19, 2020
Sam White
 

Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v1.6

2020
Miscellaneous
I previously created a C.bairdi de novo transcriptome assembly v1.6 with Trinity from all our C.bairdi taxonomically filtered RNAseq on 20200518 and decided to assess its…
May 19, 2020
Sam White
 

Transcriptome Annotation - C.bairdi Transcriptome v3.0 Using DIAMOND BLASTx on Mox

2020
Miscellaneous
As part of annotating cbai_transcriptome_v3.0.fasta from 20200518, I need to run DIAMOND BLASTx to use with Trinotate.
May 19, 2020
Sam White
 

Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v3.0

2020
Miscellaneous
I previously created a C.bairdi de novo transcriptome assembly with Trinity from all our C.bairdi pooled RNAseq (not taxonomically filtered) on 20200518 and decided to…
May 19, 2020
Sam White
 

Transcriptome Assembly - C.bairdi All Arthropoda-specific RNAseq Data with Trinity on Mox

2020
Miscellaneous
I realized I hadn’t performed taxonomic read separation from one set of RNAseq data we had. And, since I was on a transcriptome assembly kick, I figured I’d generate another …
May 18, 2020
Sam White
 

Data Wrangling - Arthropoda and Alveolata D26 Pool RNAseq FastQ Extractions

2020
Miscellaneous
After using MEGAN6 to extract Arthropoda and Alveolata reads from our RNAseq data on 20200114, I had then extracted taxonomic-specific reads and aggregated each into basic…
May 18, 2020
Sam White
 

Transcriptome Assembly - C.bairdi All Pooled RNAseq Data Without Taxonomic Filters with Trinity on Mox

2020
Miscellaneous
Steven asked that I assemble a transcriptome with just our pooled C.bairdi RNAseq data (not taxonomically filtered; see the FastQ list file linked in the Results section…
May 18, 2020
Sam White
 

Transcriptome Annotation - Trinotate C.bairdi Transcriptome v2.0 from 20200502 on Mox

2020
Miscellaneous
After performing de novo assembly on all of our Tanner crab RNAseq data (no taxonomic filter applied, either) on 20200502 and performing BLASTx annotation on 20200508, I…
May 13, 2020
Sam White
 

TransDecoder - C.bairdi Transcriptome v2.0 from 20200502 on Mox

2020
Miscellaneous
Need to run TransDecoder on Mox on the C.bairdi transcriptome v2.0 from 20200502.
May 8, 2020
Sam White
 

Transcriptome Annotation - C.bairdi Transcriptome v2.0 Using DIAMOND BLASTx on Mox

2020
Miscellaneous
As part of annotating the C.bairdi v2.0 transcriptome assembly from 20200502, I need to run DIAMOND BLASTx to use with Trinotate.
May 8, 2020
Sam White
 

Transcriptome Assessment - BUSCO Metazoa on C.bairdi v2.0 Transcriptome

2020
Miscellaneous
I previously created a C.bairdi de novo transcriptome assembly with Trinity using all existing, unfiltered (i.e. no taxonomic selection) RNAseq data on 20200502 and decided…
May 8, 2020
Sam White
 

Transcriptome Assembly - C.bairdi All RNAseq Data Without Taxonomic Filters with Trinity on Mox

2020
Miscellaneous
Steven asked that I assemble an unfiltered (i.e. no taxonomic selection) transcriptome with all of our C.bairdi RNAseq data (see the FastQ list file linked in the Results…
May 2, 2020
Sam White
 

Transcript Abundance - C.bairdi Alignment-free with Salmon Using 2020-GW Data on Mox

2020
Miscellaneous
Clarified with Steven an approach for tackling multi-condition comparisons (see this GitHub Issue). As such, I need to have individual transcript abundances for each sample…
Apr 29, 2020
Sam White
 

GO to GOslim - C.bairdi Enriched GO Terms from 20200422 DEGs

2020
Miscellaneous
After running pairwise comparisons and identify differentially expressed genes (DEGs) on 20200422 and finding enriched gene ontology terms, I decided to map the GO terms to…
Apr 27, 2020
Sam White
 

FastQC-MultiQC - Laura Spencer's QuantSeq Data

2020
Miscellaneous
Laura Spencer received her O.lurida QuantSeq data, so I put it through FastQC/MultiQC and put the pertinent info in the nightingales Google Sheet. I also moved the data to /o…
Apr 26, 2020
Sam White
 

Gene Expression - C.bairdi Pairwise DEG Comparisons with 2019 RNAseq using Trinity-Salmon-EdgeR on Mox

2020
Miscellaneous
Per a Slack request, Steven asked me to take the Genewize RNAseq data (received 2020318) through edgeR. Ran the analysis using the Trinity differential expression pipeline:
Apr 22, 2020
Sam White
 

RNAseq Reads Extractions - C.bairdi Taxonomic Reads Extractions with MEGAN6 on swoose

2020
Miscellaneous
I previously annotated reads and converted them to the MEGAN6 format RMA6 on 20200414.
Apr 19, 2020
Sam White
 

Transcript Abundance - C.bairdi Alignment-free with Salmon on Mox for Grace

2020
Miscellaneous
Per this GitHub Issue, Grace and Steven asked if I could help by generating a transcript abundance file for Grace to use with EdgeR. To do so, I used Salmon for…
Apr 15, 2020
Sam White
 

SRA Submission - C.bairdi RNAseq Data

2020
Miscellaneous
Since we received the last of our RNAseq data for this project on 20200413, I submitted all of it to the NCBI Sequencing Read Archive (SRA). Data was released today and all…
Apr 15, 2020
Sam White
 

TrimmingFastQCMultiQC---C.bairdi-RNAseq-FastQ-with-fastp-on-Mox

2020
Miscellaneous
After receiving our RNAseq data from Genewiz earlier today, needed to trim and check trimmed reads with FastQC.
Apr 14, 2020
Sam White
 

Taxonomic Assignments - C.bairdi RNAseq Using DIAMOND BLASTx on Mox and MEGAN6 Meganizer on swoose

2020
Miscellaneous
After receiving/trimming the latest round of C.bairdi RNAseq data on 20200413, need to get the data ready to perform taxonomic selection of sequencing reads. To do this, I…
Apr 14, 2020
Sam White
 

FastQC-MultiQC - C.bairdi Raw RNAseq from NWGSC

2020
Miscellaneous
Yesterday, we received the last of the RNAseq data for the C.bairdi crab project from NWGSC. FastQC, followed by MultiQC was run on the raw FastQ reads on my computer…
Apr 14, 2020
Sam White
 

Data Wrangling - Arthropoda and Alveolata Day and Treatment Taxonomic RNAseq FastQ Extractions

2020
Miscellaneous
After using MEGAN6 to extract Arthropoda and Alveolata reads from our RNAseq data on 20200330, I had then extracted taxonomic-specific reads and aggregated each into basic…
Apr 13, 2020
Sam White
 

Data Received - C.bairdi RNAseq from NWGSC

2020
Data Received
Received the C.bairdi RNAseq data from UW NWGSC that Grace submitted on 20200131. Below is a table of NWGSC sample name and corresponding labels that Grace provided. The 0/1…
Apr 13, 2020
Sam White
 

Transcriptome Annotation - Trinotate C.bairdi MEGAN6 Taxonomic-specific Trinity Assembly on Mox

2020
Miscellaneous
After performing de novo assembly on our Tanner crab MEGAN6 taxonomic-specific RNAseq data on 20200330 and performing BLASTx annotation on 20200408, I continued the…
Apr 9, 2020
Sam White
 

Transcriptome Annotation - C.bairdi MEGAN Trinity Assembly Using DIAMOND BLASTx on Mox

2020
Miscellaneous
As part of annotating the most recent transcriptome assembly from the MEGAN6 Arthropoda taxonomic-specific reads, I need to run DIAMOND BLASTx to use with Trinotate.
Apr 8, 2020
Sam White
 

Transcriptome Annotation - Trinotate Hematodinium MEGAN6 Taxonomic-specific Trinity Assembly on Mox

2020
Miscellaneous
After performing de novo assembly on our Hematodinium MEGAN6 taxonomic-specific RNAseq data on 20200330 and performing BLASTx annotation on 20200331, I continued the…
Apr 8, 2020
Sam White
 

Transdecoder - Hematodinium MEGAN6 Taxonomic-Specific Reads Assembly from 20200330

2020
Miscellaneous
Ran Trinity to de novo assembly on the the Alveolata MEGAN6 taxonomic-specific RNAseq data on 20120330 and now will begin annotating the transcriptome using TransDecoder on…
Apr 7, 2020
Sam White
 

Transdecoder - C.bairdi MEGAN6 Taxonomic-Specific Reads Assembly from 20200330

2020
Miscellaneous
Ran Trinity to de novo assembly on the the Arthropoda MEGAN6 taxonomic-specific RNAseq data on 20120330 and now will begin annotating the transcriptome using TransDecoder on…
Apr 7, 2020
Sam White
 

Transcriptome Assessment - BUSCO Metazoa on C.bairdi MEGAN Transcriptome

2020
Miscellaneous
I previously created a C.bairdi de novo transcriptome assembly with Trinity from the MEGAN6 taxonomic-specific reads for Arthropoda on 20200330 and decided to assess its…
Apr 7, 2020
Sam White
 

Transcriptome Annotation - Hematodinium MEGAN Trinity Assembly Using DIAMOND BLASTx on Mox

2020
Miscellaneous
As part of annotating the most recent transcriptome assembly from the MEGAN6 Hematodinium taxonomic-specific reads, I need to run DIAMOND BLASTx to use with Trinotate.
Mar 31, 2020
Sam White
 

Transcriptome Assessment - BUSCO Metazoa on Hematodinium MEGAN Transcriptome

2020
Miscellaneous
I previously created a C.bairdi de novo transcriptome assembly with Trinity from the MEGAN6 taxonomic-specific reads for Alveolata on 20200331 and decided to assess its…
Mar 31, 2020
Sam White
 

Transcriptome Assembly - Hematodinium with MEGAN6 Taxonomy-specific Reads with Trinity on Mox

2020
Miscellaneous
Ran a de novo assembly using the extracted reads classified under Alveolata from:
Mar 30, 2020
Sam White
 

Transcriptome Assembly - C.bairdi with MEGAN6 Taxonomy-specific Reads with Trinity on Mox

2020
Miscellaneous
Ran a de novo assembly using the extracted reads classified under Arthropoda from:
Mar 30, 2020
Sam White
 

RNAseq Reads Extractions - C.bairdi Taxonomic Reads Extractions with MEGAN6 on swoose

2020
Miscellaneous
I previously annotated reads and converted them to the MEGAN6 format RMA6 on 20200318.
Mar 30, 2020
Sam White
 

Transcriptome Annotation - C.bairdi Using DIAMOND BLASTx on Mox and MEGAN6 Meganizer on swoose

2020
Tanner Crab RNAseq
After receiving/trimming the latest round of C.bairdi RNAseq data on 20200318, need to get the data ready to perform taxonomic selection of sequencing reads. To do this, I…
Mar 18, 2020
Sam White
 

Trimming/FastQC/MultiQC - C.bairdi RNAseq FastQ with fastp on Mox

2020
Tanner Crab RNAseq
After receiving our RNAseq data from Genewiz earlier today, needed to run FastQC, trim, check trimmed reads with FastQC.
Mar 18, 2020
Sam White
 

Data Received - C.bairdi RNAseq Data from Genewiz

2020
Data Received
Tanner Crab RNAseq
We received the RNAseq data from the RNA that was sent out by Grace on 20200212.
Mar 18, 2020
Sam White
 

DNA Isolation and Quantification - C.bairdi Hemocyte Pellets in RNAlater

2020
Miscellaneous
Isolated DNA from 22 samples (see Qubit spreadsheet in “Results” below for sample IDs) using the Quick DNA/RNA Microprep Kit (ZymoResearch; PDF) according to the…
Mar 11, 2020
Sam White
 

NanoPore Sequencing - C.bairdi gDNA 6129_403_26

2020
Miscellaneous
After getting high quality gDNA from Hematodinium-infected C.bairdi hemolymph on 2020210 we decided to run some of the sample on the NanoPore MinION, since the flowcells…
Mar 11, 2020
Sam White
 

qPCR - C.bairdi RNA Check for Residual gDNA

2020
Tanner Crab RNAseq
Previuosly checked existing crab RNA for residual gDNA on 20200226 and identified samples with yields that were likely too low, as well as samples with residual gDNA. For…
Mar 10, 2020
Sam White
 

Trimming/MultiQC - Methcompare Bisulfite FastQs with fastp on Mox

2020
Miscellaneous
Steven asked me to trim a set of FastQ files, provided by Hollie Putnam, in preparation for methylation analysis using Bismark. The analysis is part of a coral project…
Mar 6, 2020
Sam White
 

RNA Isolation and Quantification - C.bairdi RNA from Hemolymph Pellets in RNAlater

2020
Tanner Crab RNAseq
Based on qPCR results testing for residual gDNA from 20200225, a set of 24 samples were identified that required DNase treatment and/or additional RNA. I opted to just…
Mar 6, 2020
Sam White
 

Data Wrangling - Create Canonical Olurida_v081 Genes FastA

2020
Miscellaneous
I finally had some time to tackle this GitHub Issue and create a canonical genes FastA file using the MAKER IDs, instead of the original contig IDs from our Olympia oyster…
Feb 28, 2020
Sam White
 

qPCR - C.bairdi RNA Check for Residual gDNA

2020
Tanner Crab RNAseq
After deciding on a primer set to use for gDNA detection on 20200225, went ahead and ran a qPCR on most of the RNA samples described in Grace’s Google Sheet. Some samples…
Feb 26, 2020
Sam White
 

qPCR - C.bairdi Primer Tests on gDNA

2020
Tanner Crab RNAseq
We received the primers I ordered on 20200220 and now need to test them to see if they detect gDNA. If yes, then they’re good candidates to assess the presence of residual…
Feb 25, 2020
Sam White
 

Primer Design - C.bairdi Primers for Checking RNA for Residual gDNA

2020
Tanner Crab RNAseq
Getting ready to run some qPCRs and first we need to confirm that our RNA is actually DNA-free. Before we can do that, we need some primers to use, so I decided to…
Feb 20, 2020
Sam White
 

DNA Isolation & Quantification - C.bairdi RNA from Samples 6212_132_9 6212_334_12 6212_485_26

2020
Tanner Crab RNAseq
Isolated DNA from three samples (see Qubit spreadsheet in “Results” below for sample IDs) using the Quick DNA/RNA Microprep Kit (ZymoResearch; PDF) according to the…
Feb 11, 2020
Sam White
 

RNA Isolation & Quantification - C.bairdi RNA from Samples 6212_132_9 6212_334_12 6212_485_26

2020
Tanner Crab RNAseq
We are supposed to get RNA sent out for sequencing today, but it turns out that a few of the designated samples have insufficient RNA in them. So, I’m going to attempt to…
Feb 11, 2020
Sam White
 

RNA Isolation & Quantification - C.bairdi RNA from Sample 6129_403_26

2020
Tanner Crab RNAseq
Since I was isolating gDNA from C.bairdi 6129_403_26 hemolymph, I figured I might as well co-isolate RNA since I was using the Quick DNA/RNA Microprep Plus Kit (ZymoResearch).
Feb 10, 2020
Sam White
 

DNA Isolation & Quantification - Additional C.bairdi gDNA from Sample 6129_403_26

2020
Miscellaneous
Earlier today I isolated gDNA from C.bairi 6129_403_26 hemolymph pellets and recovered decently intact gDNA that could be used for sequencing. However, I still need more…
Feb 10, 2020
Sam White
 

DNA Isolation, Quantification, and Gel - C.bairdi gDNA Sample 6129_403_26

2020
Miscellaneous
In order to do some genome sequencing on C.bairid and Hematodinium, we need hihg molecular weight gDNA. I attempted this twice before, using two different methods (Quick…
Feb 10, 2020
Sam White
 

Transcriptome Assessment - BUSCO Metazoa on Hematodinium MEGAN Transcriptome

2020
Tanner Crab RNAseq
I previously created a Hematodinium de novo transcriptome assembly with Trinity from the MEGAN6 taxonomic-specific reads for Alveolata on 20200122 and decided to assess its…
Feb 7, 2020
Sam White
 

Transcriptome Assessment - BUSCO Metazoa on C.bairdi MEGAN Transcriptome

2020
Tanner Crab RNAseq
I previously created a C.bairdi de novo transcriptome assembly with Trinity from the MEGAN6 taxonomic-specific reads for Arthropoda on 20200122 and decided to assess its…
Feb 7, 2020
Sam White
 

Gene Expression - Hematodinium MEGAN6 with Trinity and EdgeR

2020
Miscellaneous
After completing annotation of the Hematodinium MEGAN6 taxonomic-specific Trinity assembly using Trinotate on 20200126, I performed differential gene expression analysis and…
Feb 7, 2020
Sam White
 

Gene Expression - C.bairdi MEGAN6 with Trinity and EdgeR

2020
Tanner Crab RNAseq
After completing annotation of the C.bairdi MEGAN6 taxonomic-specific Trinity assembly using Trinotate on 20200126, I performed differential gene expression analysis and…
Feb 7, 2020
Sam White
 

Data Wrangling - Arthropoda and Alveolata Day and Treatment Taxonomic RNAseq FastQ Extractions

2020
Tanner Crab RNAseq
After using MEGAN6 to extract Arthropoda and Alveolata reads from our RNAseq data on 20200114, I had then extracted taxonomic-specific reads and aggregated each into basic…
Jan 31, 2020
Sam White
 

DNA Isolation and Quantification - C.bairdi Hemocyte Pellets in RNAlater

2020
Miscellaneous
Isolated DNA from 56 samples (see Qubit spreadsheet in “Results” below for sample IDs) using the Quick DNA/RNA Microprep Kit (ZymoResearch; PDF) according to the…
Jan 28, 2020
Sam White
 

Transcriptome Annotation - Trinotate Hematodinium MEGAN6 Taxonomic-specific Trinity Assembly on Mox

2020
Tanner Crab RNAseq
After performing de novo assembly on our Hematodinium MEGAN6 taxonomic-specific RNAseq data on 20200122 and performing BLASTx annotation on 20200123, I continued the…
Jan 26, 2020
Sam White
 

Transcriptome Annotation - Trinotate C.bairdi MEGAN6 Taxonomic-specific Trinity Assembly on Mox

2020
Tanner Crab RNAseq
After performing de novo assembly on our Tanner crab MEGAN6 taxonomic-specific RNAseq data on 20200122 and performing BLASTx annotation on 20200123, I continued the…
Jan 26, 2020
Sam White
 

RNA Isolation and Quantification - C.bairdi Hemocyte Pellets in RNAlater

2020
Tanner Crab RNAseq
Isolated RNA from the following hemolymph pellet samples:
Jan 26, 2020
Sam White
 

RNA Isolation and Quantification - C.bairdi Hemocyte Pellets in RNAlater

2020
Tanner Crab RNAseq
Isolated RNA from the following hemolymph pellet samples:
Jan 24, 2020
Sam White
 

Transdecoder - Hematodinium MEGAN6 Taxonomic-Specific Reads Assembly from 20200122

2020
Miscellaneous
Ran Trinity to de novo assembly on the the C.bairdi MEGAN6 taxonomic-specific RNAseq data on 201200122 and now will begin annotating the transcriptome using TransDecoder on…
Jan 23, 2020
Sam White
 

Transdecoder - C.bairdi MEGAN6 Taxonomic-Specific Reads Assembly from 20200122

2020
Tanner Crab RNAseq
Ran Trinity to de novo assembly on the the Hematodinium MEGAN6 taxonomic-specific RNAseq data on 201200122 and now will begin annotating the transcriptome using TransDecoder…
Jan 23, 2020
Sam White
 

Transcriptome Annotation - Hematodinium MEGAN Trinity Assembly Using DIAMOND BLASTx on Mox

2020
Miscellaneous
As part of annotating the transcriptome assembly from the MEGAN6 Hematodinium taxonomic-specific reads, I need to run DIAMOND BLASTx to use with Trinotate.
Jan 23, 2020
Sam White
 

Transcriptome Annotation - C.bairdi MEGAN Trinity Assembly Using DIAMOND BLASTx on Mox

2020
Tanner Crab RNAseq
As part of annotating the transcriptome assembly from the MEGAN6 C.bairdi taxonomic-specific reads, I need to run DIAMOND BLASTx to use with Trinotate.
Jan 23, 2020
Sam White
 

RNA Isolation and Quantification - C.bairdi Hemocyte Pellets in RNAlater Troubleshooting

2020
Tanner Crab RNAseq
After the failure to obtain RNA from any C.bairdi hemocytes pellets (out of 24 samples processed) on 20200117, I decided to isolate RNA from just a subset of that group to…
Jan 23, 2020
Sam White
 

DNA Quality Assessment - Agarose Gel for C.bairdi 20102558-2729 gDNA from 20200122

2020
Miscellaneous
Earlier today, I isolated gDNA from C.bairdi 20102558-2729 ethanol-preserved muscle tissue using the Quick DNA/RNA MicroPrep Plus Kit (ZymoResearch) and prepared the tissue…
Jan 22, 2020
Sam White
 

Data Wrangling - Arthropoda and Alveolata Taxonomic RNAseq FastQ Extractions

2020
Tanner Crab RNAseq
After using MEGAN6 to extract Arthropoda and Alveolata reads from our RNAseq data on 20200114 (for reference, these include RNAseq data using a newly established…
Jan 22, 2020
Sam White
 

DNA Isolation - C.bairdi 20102558-2729 EtOH-preserved Tissue via Three Variations Using Quick DNA-RNA MicroPrep Kit

2020
Miscellaneous
Previously, I isolated gDNA from a C.bairdi EtOH-preserved muscle sample (20102558-2729) on 20200108 using the E.Z.N.A. Mollusc DNA Kit (Omega). Although the yields were…
Jan 22, 2020
Sam White
 

Transcriptome Assembly - Hematodinium with MEGAN6 Taxonomy-specific Reads with Trinity on Mox

2020
Miscellaneous
Ran a de novo assembly using the extracted reads classified under Alveolata from 20200122 The assembly was performed with Trinity on Mox.
Jan 22, 2020
Sam White
 

Transcriptome Assembly - C.bairdi with MEGAN6 Taxonomy-specific Reads with Trinity on Mox

2020
Tanner Crab RNAseq
Ran a de novo assembly using the extracted reads classified under Arthropoda from 20200122 (for reference, these include RNAseq data using a newly established “shorthand”…
Jan 22, 2020
Sam White
 

DNA Isolation and Quantification - C.bairdi Hemolymph Pellets in RNAlater

2020
Miscellaneous
Isolated DNA from the following 23 samples:
Jan 17, 2020
Sam White
 

RNA Isolation and Quantification - C.bairdi Hemolymph Pellets in RNAlater

2020
Tanner Crab RNAseq
TL;DR - Recovered absolutely no RNA from any sample! However, I did recover DNA from each sample.
Jan 17, 2020
Sam White
 

RNAseq Reads Extractions - C.bairdi Taxonomic Reads Extractions with MEGAN6 on swoose

2020
Tanner Crab RNAseq
I previously ran BLASTx and “meganized” the output DAA files on 20200103 (for reference, these include RNAseq data using a newly established “shorthand”: 2018, 2019) and now…
Jan 14, 2020
Sam White
 

Lab Maintenance - Cluster UPS Battery Replacement

2020
Miscellaneous
Replaced the batteries on one of the APC uninterruptable power supplies (UPS) on our local server cabinet.
Jan 10, 2020
Sam White
 

NanoPore Sequencing - C.bairdi gDNA Sample 20102558-2729

2020
Miscellaneous
I performed the initial Lambda sequencing test on 20200107 and everything went smoothly, so I’m ready to give the NanoPore (ONT) MinION a run with an actual sample!
Jan 9, 2020
Sam White
 

DNA Quality Assessment - Agarose Gel and NanoDrop on C.bairdi gDNA

2020
Miscellaneous
I isolated C.bairdi gDNA yesterday (20200108) and now want to get an idea if it’s any good (i.e. no contaminants, high molecule weight).
Jan 9, 2020
Sam White
 

DNA Isolation and Quantification - C.bairdi gDNA from EtOH Preserved Tissue

2020
Miscellaneous
I isolated gDNA from ethanol-preserved C.bairdi muscle tissue from sample 20102558-2729 (SPNO-ReferenceNO). This sample was chosen as it had 0 in the SMEAR_result and BCS_PCR…
Jan 8, 2020
Sam White
 

NanoPore Sequencing - Initial NanoPore MinION Lambda Sequencing Test

2020
Miscellaneous
We recently acquired a NanoPore MinION sequencer, FLO-MIN106 flow cell and the Rapid Sequencing Kit (SQK-RAD004). The NanoPore website provides a pretty thorough an…
Jan 7, 2020
Sam White
 

Transcriptome Annotation - C.bairdi Using DIAMOND BLASTx on Mox and MEGAN6 Meganizer

2020
Tanner Crab RNAseq
Although I previously annotated our C.bairdi transcriptome from 20191218, I realized that the assembly and annotations were combine infected/uninfected samples, possibly…
Jan 3, 2020
Sam White
 

Reagent Prep - RNA Pico Ladder Aliquoting and Testing

2020
Reagent Prep
Created aliquots of RNA Pico Ladder received on 20191101, per the manufacturer’s instructions. Created single-use aliquots of 1.5uL and stored at -80oC:
Jan 2, 2020
Sam White
 

Transcriptome Annotation - C.bairdi Trinity Assembly Trinotate on Mox

2019
Tanner Crab RNAseq
After performing de novo assembly on our Tanner crab RNAseq data on 20191218 and performing BLASTx annotation on 20191224, I continued the annotation process by running Trino…
Dec 25, 2019
Sam White
 

Transcriptome Annotation - C.bairdi Trinity Assembly BLASTx on Mox

2019
Tanner Crab RNAseq
In preparation for complete transcriptome annotation of the C.bairdi de novo assembly fro 20191218, I needed to run BLASTx. The assembly was BLASTed against the SwissProt…
Dec 24, 2019
Sam White
 

Transdecoder - C.bairdi De Novo Transcriptome from 20191218 on Mox

2019
Tanner Crab RNAseq
Ran Trinity to de novo assemble the C.bairdi RNAseq data we had on 20191218 and now will begin annotating the transcriptome using TransDecoder on Mox.
Dec 20, 2019
Sam White
 

Transcriptome Assembly - C.bairdi Trimmed RNAseq Using Trinity on Mox

2019
Tanner Crab RNAseq
Earlier today, I trimmed our existing C.bairdi RNAseq data, as part of producing generating a transcriptome (per this GitHub issue). After trimming, I performed a de novo ass…
Dec 18, 2019
Sam White
 

Trimming/FastQC/MultiQC - C.bairdi RNAseq FastQ with fastp on Mox

2019
Tanner Crab RNAseq
Grace/Steven asked me to generate a de novo transcriptome assembly of our current C.bairdi RNAseq data in this GitHub issue. As part of that, I needed to quality trim the…
Dec 18, 2019
Sam White
 

Data Wrangling - Olurida_v081 UTR GFFs and Intergenic, Intron BED files

2019
Miscellaneous
After a meeting last week, we realized we needed to update the paper-oly-mbdbs-gen GitHub repo with the most current versions of feature files we had.
Dec 14, 2019
Sam White
 

Samples Received - Pacific Oyster Tissues from Hawaii (Maria Haws) from High and Low pCO2

2019
Samples Received
We received frozen Crassostrea gigas tissues from Maria Haws in Hawaii, as part of a pCO2 experiment. Tissues include:
Dec 10, 2019
Sam White
 

Data Wrangling - Renaming, Splitting, and Feature Counts of Updated Pgenerosa_v074 GenSAS Merged GFF

2019
Geoduck Genome Sequencing
In the final GFF from our GenSAS Pgenerosa_v074.a4 annotation, we noticed that there were no repeat motifs/sequences identified on Scaffold 01. The remaining scaffolds all…
Dec 3, 2019
Sam White
 

PCR - Crassostrea gigas and sikamea Mantle gDNA from Marinelli Shellfish Company

2019
Miscellaneous
I ran this PCR a couple of times before and, embarrassingly, I had ordered/used the wrong primers.
Dec 3, 2019
Sam White
 

Samples Received - C.bairdi Hemolymph and Tissue in Ethanol from Pam Jensen

2019
Samples Received
Pam Jensen (NOAA) brought by a variety of hemolymph and tissues stored in ethanol to use for DNA sequencing with the new MinION (Oxford Nanopore) to help aid our…
Nov 27, 2019
Sam White
 

qPCR - Geoduck hemolymph and hemocyte cDNA with vitellogenin primers

2019
Miscellaneous
Previously isolated RNA on 20191125 and made cDNA on 20191126 from some geoduck hemolymph and hemocyte samples that Shelly asked me to run qPCRs on.
Nov 27, 2019
Sam White
 

Reverse Transcription - P.generosa DNased Hemolypmh and Hemocyte RNA from 20191125

2019
Miscellaneous
Performed reverse transcription on the DNased hemolymph and hemocyte RNA from yesterday.
Nov 26, 2019
Sam White
 

RNA Isolation and Quantification - Geoduck hemolymph and hemocyte samples

2019
Miscellaneous
Shelly asked me to isolate RNA and run some qPCRs on the following samples:
Nov 25, 2019
Sam White
 

PCR - Crassostrea gigas and sikamea Mantle gDNA from Marinellie Shellfish Company - No Multiplex

2019
Miscellaneous
Since the results I obtained on my final attempt to get this to work failed, I decided to double-check the primer sequences.
Nov 21, 2019
Sam White
 

PCR - Crassostrea gigas and sikamea Mantle gDNA from Marinelli Shellfish Company

2019
Miscellaneous
Since the results I obtained on my final attempt to get this to work failed, I decided to double-check the primer sequences.
Nov 21, 2019
Sam White
 

Data Wrangling - Rename Pgenerosa_v074 Bismark Coverage Files Scaffold Names

2019
Geoduck Genome Sequencing
After a meeting today, Steven and Hollie realized that the Bismark coverage files were still using the old scaffold names, stemming from the Pgenerosa_v074 naming. I’d previo…
Nov 20, 2019
Sam White
 

PCR - Crassostrea gigas and sikamea Mantle gDNA from Marinelli Shellfish Company

2019
Miscellaneous
Since the results I obtained on my final attempt to get this to work failed, I decided to double-check the primer sequences.
Nov 19, 2019
Sam White
 

DNA Isolation and Quantification - Crassostrea gigas and Crassostrea sikamea Mantle Tissue from Marinelli Shellfish Company

2019
Miscellaneous
Isolated DNA from the C.gigas and C.sikamea samples we received from Marinelli Shellfish Company on 20191030 using DNAzol.
Nov 19, 2019
Sam White
 

Data Wrangling - Additional Features Stats for Panopea-generosa-v1.0

2019
Geoduck Genome Sequencing
Although I’d previously generated some feature stats for this genome annotation (see 20191029), we decided we wanted to get some additional info, similar to that of Table 1 i…
Nov 6, 2019
Sam White
 

Data Wrangling - Rename Pgenerosa_v074 Files and Scaffolds

2019
Geoduck Genome Sequencing
Continuing to organizing files for a manuscript dealing with the geoduck genome assembly/annotation we’ve done, we decided to rename the files as well as rename the…
Nov 5, 2019
Sam White
 

Data Wrangling - Splitting BAM by Size for Upload to OSF

2019
Geoduck Genome Sequencing
We’re in the process of organizing files for a manuscript dealing with the geoduck genome assembly/annotation we’ve done. As part of that, we need the Stringtie BAM file…
Oct 31, 2019
Sam White
 

Samples Received - Marinelli Shellfish Company C.gigas and C.sikamea Oysters

2019
Miscellaneous
Steven was recently contacted by Marinelli Shellfish Company to see if we could help them determine if some oysters they had were Crassostrea gigas (Pacific oyster) or Crasso…
Oct 30, 2019
Sam White
 

Data Wrangling - Create Panopea-generosa-vv0.74.a4 Intron and Intergenic BED Files

2019
Geoduck Genome Sequencing
Since generating an updated Pgenerosa_v074 annotation, we also needed updated intergenic and intron bed files to put in the OSF repository for this project.
Oct 30, 2019
Sam White
 

Genome Feature Counts - Panopea-generosa-vv0.74.a4

2019
Geoduck Genome Sequencing
Due to a bug with GenSAS, the final GFF generated by their system to did not properly merge all of the repeats data properly. The repeats data below should be ignored! It…
Oct 29, 2019
Sam White
 

FastQC-MultiQC - C.bairdi RNAseq Day 12 26 Infected Uninfected

2019
Tanner Crab RNAseq
After receiving the rest of the crab data and concatenating it all together, I ran FastQC and MultiQC on the FastQ files.
Oct 24, 2019
Sam White
 

Data Received - C.bairdi RNAseq Day9-12-26 Infected-Uninfected

2019
Tanner Crab RNAseq
Data Received
Previously, we “received” this data, but it turns out it was incomplete (see 20191003).
Oct 24, 2019
Sam White
 

Lab Maintenance - Cluster UPS Battery Replacement

2019
Miscellaneous
Replaced the batteries on one of the APC uninterruptable power supplies (UPS) on our local server cabinet.
Oct 22, 2019
Sam White
 

Metagenomics Annotation - P.generosa Water Samples with MEGAN6

2019
Miscellaneous
After running DIAMOND BLASTx and MEGANIZER on these samples on 20190925 to assess taxonomy info, I began the analyses/visualization of this data with MEGAN6.
Oct 14, 2019
Sam White
 

Data Received - C.bairdi RNAseq Day9-12-26 Infected-Uninfected

2019
Tanner Crab RNAseq
Finally received the RNAseq data back from NWGC that we submitted on 20190521!
Oct 3, 2019
Sam White
 

Genome Annotation - Pgenerosa_v074 a4 Using GenSAS

2019
Geoduck Genome Sequencing
I’d previously annotated our Pgenerosa_v074 with GenSAS, but did so using limited options as we were (and still are) in need of an annotated genome to use for methylation…
Sep 28, 2019
Sam White
 

Metagenomics Annotation - P.generosa Water Samples Using DIAMOND BLASTx on Mox

2019
Miscellaneous
We recently had a meeting with Emma and Brook about the progress of this metagenomics project and Brook suggested trying out MEGAN6 as user-friendly way to get these samples…
Sep 25, 2019
Sam White
 

Trimming/FastQC/MultiQC - P.generosa EPI FastQs with FASTP on Mox

2019
Miscellaneous
Steven noticed that the M-Bias plots generated by Bismark from these files was a little wonky and asked that I try trimming them a bit more. The files were originally…
Sep 23, 2019
Sam White
 

SRA Submission - Hollie's Juvenile OA BS-seq Data

2019
SRA Submissions
Submitted sequencing data (52 samples; see table below) from Hollie’s BS-seq project looking at differences in DNA methylation between juvenile geoduck exposed to different…
Sep 18, 2019
Sam White
 

Data Wrangling - Pgenerosa_v074.a3 Annotation Genome Repeats Compostion

2019
Geoduck Genome Sequencing
Needed to pull some numbers on repeats in our Pgenerosa_v074.a3 GenSAS annotation (from 20190710) for the manuscript we’re putting together.
Sep 5, 2019
Sam White
 

Data Wrangling - Pgenerosa_v074.a3 Annotation Genome Feature Sequence Lengths

2019
Geoduck Genome Sequencing
The GenSAS Pgenerosa_v074 annotation from 20190710 (referred to as: Panopea-generosa-vv0.74.a3) recently completed (after nearly a month of running).
Sep 4, 2019
Sam White
 

Data Wrangling - Panopea generosa Genome Feature Sequence Lengths

2019
Geoduck Genome Sequencing
In preparation for a paper we’re writing, we needed some summary stats on the various genome assembly feature sequences. I determined the max/min, mean, and median sequence…
Aug 26, 2019
Sam White
 

Data Wrangling - Create a CpG GFF from Pgenerosa_v074 using EMBOSS fuzznuc on Swoose

2019
Geoduck Genome Sequencing
Steven wanted me to create a CpG GFF for use in IGV visulations for continued Pgenerosa_v074 analysis. I did that by running the EMBOSS tool fuzznuc:
Aug 21, 2019
Sam White
 

Genome Annotation - Pgenerosa_v074 MAKER on Mox with Stringtie Transcripts GFF

2019
Geoduck Genome Sequencing
For reference, this annotation will be referred to as Pgenerosa_v074.1.
Aug 19, 2019
Sam White
 

Genome Comparison - Pgenerosa_v074 vs Pgenerosa_v070 with MUMmer Promer on Mox

2019
Miscellaneous
In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…
Aug 13, 2019
Sam White
 

Genome Comparison - Pgenerosa_v074 vs S.glomerata NCBI with MUMmer Promer on Mox

2019
Miscellaneous
In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…
Aug 13, 2019
Sam White
 

Genome Comparison - Pgenerosa_v074 vs M.yessoensis NCBI with MUMmer Promer on Mox

2019
Miscellaneous
In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…
Aug 13, 2019
Sam White
 

Genome Comparison - Pgenerosa_v074 vs H.sapiens NCBI with MUMmer Promer on Mox

2019
Miscellaneous
In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…
Aug 13, 2019
Sam White
 

Genome Comparison - Pgenerosa_v074 vs C.virginica NCBI with MUMmer Promer on Mox

2019
Miscellaneous
In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…
Aug 13, 2019
Sam White
 

Genome Comparison - Pgenerosa_v074 vs C.gigas NCBI with MUMmer Promer on Mox

2019
Miscellaneous
In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…
Aug 13, 2019
Sam White
 

Genome Comparison - Pgenerosa_v074 vs Pgenerosa_v070 with MUMmer on Mox

2019
Miscellaneous
In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…
Aug 7, 2019
Sam White
 

Genome Comparison - Pgenerosa_v074 vs Pgenerosa_v074 with MUMmer on Mox

2019
Miscellaneous
In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…
Aug 7, 2019
Sam White
 

Genome Comparison - Pgenerosa_v074 vs S.glomerata NCBI with MUMmer on Mox

2019
Miscellaneous
In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…
Aug 7, 2019
Sam White
 

Genome Comparison - Pgenerosa_v074 vs M.yessoensis NCBI with MUMmer on Mox

2019
Miscellaneous
In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…
Aug 7, 2019
Sam White
 

Genome Comparison - Pgenerosa_v074 vs C.gigas NCBI with MUMmer on Mox

2019
Miscellaneous
In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…
Aug 7, 2019
Sam White
 

Genome Comparison - Pgenerosa_v074 vs H.sapiens NCBI with MUMmer on Mox

2019
Miscellaneous
In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…
Aug 7, 2019
Sam White
 

Genome Comparison - Pgenerosa_v074 vs C.virginica NCBI with MUMmer on Mox

2019
Miscellaneous
In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…
Aug 6, 2019
Sam White
 

RepeatMasker - Pgenerosa_v070 for Transposable Element ID on Roadrunner

2019
Geoduck Genome Sequencing
Continuing our various attempts at annotating our geoduck genome assemblies, I will be re-annotating our Pgenerosa_v070 (see Genome Resources GitHub wiki for deets) and…
Aug 6, 2019
Sam White
 

Data Wrangling - FastA Splitting With faSplit

2019
Miscellaneous
Steven posted an issue on GitHub regarding splitting a FastA file into multiple sequences. Specifically, he wanted a single, large FastA sequence (~89Mbp) split into smaller…
Jul 31, 2019
Sam White
 

Data Summary - P.generosa Transcriptome Assemblies Stats

2019
Miscellaneous
In our continuing quest to wrangle the geoduck transcriptome assemblies we have, I was tasked with compiling assembly stats for our various assemblies. The table below…
Jul 29, 2019
Sam White
 

Transcriptome Compression - P.generosa Transcriptome Assemblies Using CD-Hit-est on Mox

2019
Miscellaneous
In continued attempts to get a grasp on the geoduck transcriptome size, I decided to “compress” our various assemblies by clustering similar transcripts in each assembly in…
Jul 29, 2019
Sam White
 

Genome Annotation - Pgenerosa_v074 Transcript Isoform ID with Stringtie on Mox

2019
Geoduck Genome Sequencing
After annotating Pgenerosa_v070 and comparing feature counts, there was a drastic difference between the two genome versions. Additionally, both of those genomes ended up…
Jul 23, 2019
Sam White
 

Genome Annotation - Pgenerosa_v070 Transcript Isoform ID with Stringtie on Mox

2019
Geoduck Genome Sequencing
After annotating Pgenerosa_v074 and comparing feature counts, there was a drastic difference between the two genome versions. Additionally, both of those genomes ended up…
Jul 23, 2019
Sam White
 

Genome Annotation - Pgenerosa_v074 Hisat2 Transcript Isoform Index

2019
Geoduck Genome Sequencing
Essentially, the steps below (which is what was done here) are needed to prepare files for use with Stringtie:
Jul 23, 2019
Sam White
 

Genome Annotation - Pgenerosa_v070 Hisat2 Transcript Isoform Index

2019
Geoduck Genome Sequencing
This is the first step in getting transcript isoform annotations. The annotations and alignments that will be generated with Stringtie will be used to help us get a better…
Jul 23, 2019
Sam White
 

Genome Annotation - Pgenerosa_v070 and v074 Top 18 Scaffolds Feature Count Comparisons

2019
Geoduck Genome Sequencing
After annotating Pgenerosa_v074 on 20190701, we noticed a large discrepancy in the number of transcripts that MAKER identified, compared to Pgenerosa_v070. As a reminder…
Jul 22, 2019
Sam White
 

Genome Annotation - O.lurida 20190709-v081 Transcript Isoform ID with Stringtie on Mox

2019
Olympia Oyster Genome Sequencing
Earlier today, I generated the necessary Hista2 index, which incorporated splice sites and exons, for use with Stringtie in order to identify transcript isoforms in our 20190…
Jul 16, 2019
Sam White
 

Genome Annotation - O.lurida 20190709-v081 Hisat2 Transcript Isoform Index

2019
Olympia Oyster Genome Sequencing
Last week I re-annotated our Olurida_v081 genome using tissue-specific transcriptomes. The MAKER annotations don’t yield transcript isoforms, so this is the first part of…
Jul 16, 2019
Sam White
 

Genome Assessment - BUSCO Metazoa on Pgenerosa_v074 on Mox

2019
Geoduck Genome Sequencing
Ran BUSCO on Mox for our Pgenerosa_v74 genome assembly to assess “completeness”. This is the assembly that only has the longest 18 scaffolds (the scaffolds hand-curated by…
Jul 10, 2019
Sam White
 

Genome Assessment - BUSCO Metazoa on Pgenerosa_v70 on Mox

2019
Geoduck Genome Sequencing
Ran BUSCO on Mox for our Pgenerosa_v70 genome assembly to assess “completeness”.
Jul 10, 2019
Sam White
 

Genome Annotation - Pgenerosa_v071 Using GenSAS

2019
Geoduck Genome Sequencing
In our various attempts to get the Panopea generosa genome annotated in such a manner that we’re comfortable with (the previous annotation attempts we’re lacking any…
Jul 10, 2019
Sam White
 

Genome Annotation - Pgenerosa_v074 Using GenSAS

2019
Geoduck Genome Sequencing
In our various attempts to get the Panopea generosa genome annotated in such a manner that we’re comfortable with (the previous annotation attempts we’re lacking any…
Jul 10, 2019
Sam White
 

Genome Annotation - Olurida_v081 with MAKER and Tissue-specific Transcriptomes on Mox

2019
Olympia Oyster Genome Sequencing
I previously annotated our Olurida_v081 genome with MAKER using our “canonical” transcriptome, Olurida_transcriptome_v3.fasta as the EST evidence utilized by MAKER. A discuss…
Jul 9, 2019
Sam White
 

Genome Annotation - Pgenerosa_v074 MAKER on Mox

2019
Geoduck Genome Sequencing
I previously created a subset of the Pgenerosa_v070 genome assembly that contains just the largest 18 scaffolds (these scaffolds were produced by Phase Genomics, utilizing…
Jul 1, 2019
Sam White
 

Transcriptome Annotation - Geoduck Gonad with Transdecoder on Mox

2019
Miscellaneous
Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Jun 27, 2019
Sam White
 

Transcriptome Annotation - Geoduck Juvenile Super Low OA EPI115 with Transdecoder on Mox

2019
Miscellaneous
Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Jun 27, 2019
Sam White
 

Transcriptome Annotation - Geoduck Super Low OA EPI116 with Transdecoder on Mox

2019
Miscellaneous
Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Jun 27, 2019
Sam White
 

Transcriptome Annotation - Geoduck Ctenidia with Transdecoder on Mox

2019
Miscellaneous
Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Jun 27, 2019
Sam White
 

Transcriptome Annotation - Geoduck Juvenile Ambient OA EPI124 with Transdecoder on Mox

2019
Miscellaneous
Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Jun 27, 2019
Sam White
 

Transcriptome Annotation - Geoduck Larvae Day5 EPI99 with Transdecoder on Mox

2019
Miscellaneous
Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Jun 27, 2019
Sam White
 

Transcriptome Annotation - Geoduck Juvenile Ambient OA EPI123 with Transdecoder on Mox

2019
Miscellaneous
Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Jun 27, 2019
Sam White
 

RepeatModeler - Pgenerosa_v074 for MAKER Annotation on Emu

2019
Miscellaneous
Yesterday (20190625) I generated a subset of the first 18 FastA sequences from the Pgenerosa_v070.fa file. This subset has been designated as Pgenerosa_v074 by Steven. It’s…
Jun 26, 2019
Sam White
 

RepeatMasker - Pgenerosa_v074 for Transposable Element ID on Roadrunner

2019
Miscellaneous
Yesterday (20190625) I generated a subset of the first 18 FastA sequences from the Pgenerosa_v070.fa file. This subset has been designated as Pgenerosa_v074 by Steven. It’s…
Jun 26, 2019
Sam White
 

Data Received - C.virginica Mantle MBD-BSseq from ZymoResearch

2019
Miscellaneous
We received the BSseq data from ZymoResearch today. Samples were submitted on 20190326. The samples constituted 24 Crassostrea virginica mantle samples which were prepared…
Jun 26, 2019
Sam White
 

Data Wrangling - FastA Subsetting of Pgenerosa_v070.fa Using samtools faidx

2019
Miscellaneous
Steven asked to subset the Pgenerosa_v070.fa (2.1GB) in this GitHub Issue #705. In that issue, it was determined that a significant portion of the sequencing data that was…
Jun 25, 2019
Sam White
 

Genome Annotation - O.lurida (v081) Transcript Isoform ID with Stringtie on Mox

2019
Olympia Oyster Genome Sequencing
Earlier today, I generated the necessary Hista2 index, which incorporated splice sites and exons, for use with Stringtie in order to identify transcript isoforms in our Oluri…
Jun 25, 2019
Sam White
 

Genome Annotation - O.lurida (v081) Hisat2 Transcript Isoforms Index

2019
Olympia Oyster Genome Sequencing
Per this thread in Slack, we realized that the “final” annotation of the Olurida_v081 genome only seemed to have singular mRNA annotations and no apparent isoforms. As such…
Jun 25, 2019
Sam White
 

Metagenomics - Refining Anvio Binning

2019
Miscellaneous
UPDATE 20220121: THIS IS AN INCOMPLETE POST AND IS ONLY POSTED FOR POSTERITY.
Jun 19, 2019
Sam White
 

Metagenomics - Taxonomic Diversity and Sequencing Coverage with MEGAHIT BLASTx and Krona Plots

2019
Miscellaneous
After a meeting on this project around the middle of May, we decided to try various approaches to assessing the metagenome. One aspect was to add coverage sequencing…
Jun 12, 2019
Sam White
 

Data Wrangling - Create Pgenerosa_v070 GFFs

2019
Geoduck Genome Sequencing
Since the MAKER genome annotation of our Pgenerosa_v070 genome assembly finally completed last week, I decided to separate out the various features into separate GFF files…
May 23, 2019
Sam White
 

Sample Submission - Tanner Crab Infected vs Uninfected RNAseq

2019
Tanner Crab RNAseq
Samples Submitted
After reviewing our options for sample pooling, we decided to do a comparison of Infected vs. Uninfected crabs.
May 21, 2019
Sam White
 

Metagenomics - BLASTx of Individual Water Sample MEGAHIT Assemblies on Mox

2019
Miscellaneous
After a meeting on this project yesterda, we decided to try a few things to continue with various approaches to assessing the metagenome. One of the approaches is to run…
May 16, 2019
Sam White
 

Library Decisions - C.bairdi RNAs for Library Pools

2019
Tanner Crab RNAseq
I isolated a bunch of tanner crab RNA on 20190430 and Steven asked me to try to figure out some options for RNAseq libray pools.
May 14, 2019
Sam White
 

FastQC-MultiQC - Additional C.gigas WGBS Sequencing Data from Genewiz Received 20190501

2019
Miscellaneous
Earlier today, we received the additional G.gigas sequencing data from Genewiz. Wanted to run through FastQC again and get an updated report for each data set. Admittedly…
May 1, 2019
Sam White
 

Data Received - Additional C.gigas Whole Genome Bisulfite Sequencing Data from Genewiz

2019
Miscellaneous
The FastQC analysis of the intitial data we received from Genewiz (on 20190408)showed consistent failures in the “Per Tile Sequence Quality” for all of Roberto’s Crassostrea…
May 1, 2019
Sam White
 

RNA Isolation and Quantification - C.bairdi Hemolymph Pellet in RNAlater

2019
Miscellaneous
After the success we had isolating RNA using the Quick-DNA/RNA Microprep Plus Kit (ZymoResearch), Steven had me isolate RNA from a list of ~117 samples. Of that list, I was…
Apr 30, 2019
Sam White
 

SRA Submission - P.generosa 10x Genomics Sequencing Data

2019
Geoduck Genome Sequencing
Submitted the 10x Genomics sequencing files to the NCBI short read archive (SRA) that was performed by Illumina, as part of their generous offer to use geoduck samples to…
Apr 24, 2019
Sam White
 

Data Analysis - C.virginica MBD Sequencing Coverage

2019
Miscellaneous
A while ago, Steven tasked me with assessing some questions related to the sequencing coverage we get doing MBD-BSseq in this GitHub issue. At the heart of it all was really…
Apr 18, 2019
Sam White
 

Metagenomics Annotation - P.generosa Water Samples Using BLASTn on Mox and KronaTools Visualization to Compare pH Treatments

2019
Miscellaneous
Nearing the end of this quick metagenomics comparison of taxonomic differences between the two pH treatments (pH=7.1 and pH=8.2). Previously ran:
Apr 16, 2019
Sam White
 

Metagenomics Gene Prediction - P.generosa Water Samples Using MetaGeneMark on Mox to Compare pH Treatments

2019
Miscellaneous
Continuing with a relatively quick comparison of pH treatments (pH=7.1 vs. pH=8.2), I wanted to run gene prediction on the MEGAHIT assemblies I made yesterday. I ran MetaGene…
Apr 16, 2019
Sam White
 

FastQC - WGBS Sequencing Data from Genewiz Received 20190408

2019
Miscellaneous
We received whole genome bisulfite sequencing (WGBS) data from Genewiz last week on 20190408, so ran FastQC on the files on my computer (swoose). FastQC results will be…
Apr 15, 2019
Sam White
 

Metagenome Assemblies - P.generosa Water Samples Trimmed HiSeqX Data Using Megahit on Mox to Compare pH Treatments

2019
Miscellaneous
A report involving our work on the geoduck water metagenomics is due later this week and our in-depth analysis for this project using Anvi’o is likely to require at least…
Apr 15, 2019
Sam White
 

RNA Isolation and Quantification - Crab Hemolypmh Using Quick-DNA-RNA Microprep Plus Kit

2019
Tanner Crab RNAseq
In the continuing struggle to isolate RNA from the Chionoecetes bairdi hemolymph preserved in RNAlater, Pam managed to find the Quick-DNA-RNA Microprep Plus Kit…
Apr 11, 2019
Sam White
 

Transcriptome Assembly - Geoduck Tissue-specific Assembly Larvae Day5 EPI99 with HiSeq and NovaSeq Data on Mox

2019
Miscellaneous
I previously assembled and annotated P.generosa larval Day 5 transcriptome (20190318 - mislabeled as Juvenile Day 5 in my previous notebook entries) using just our HiSeq…
Apr 9, 2019
Sam White
 

Transcriptome Assembly - Geoduck Tissue-specific Assembly Gonad HiSeq and NovaSeq Data on Mox

2019
Miscellaneous
I previously assembled and annotated P.generosa gonad transcriptome (20190318) using just our HiSeq data from our Illumina collaboration. This was a an oversight, as I…
Apr 9, 2019
Sam White
 

Transcriptome Assembly - Geoduck Tissue-specific Assembly Juvenile Ambient OA EPI124 with HiSeq and NovaSeq Data on Mox

2019
Miscellaneous
Ran a de novo assembly on our HiSeq and NovaSeq data from Hollie’s juvenile EPI 124 sample “ambient OA”. This was done for Christian to use in some long, non-coding RNA…
Apr 9, 2019
Sam White
 

Transcriptome Assembly - Geoduck Tissue-specific Assembly Juvenile Ambient OA EPI123 with HiSeq Data on Mox

2019
Miscellaneous
Ran a de novo assembly on our HiSeq data from Hollie’s juvenile EPI 123 sample “ambient OA”. This was done for Christian to use in some long, non-coding RNA (lncRNA) analysis.
Apr 9, 2019
Sam White
 

Transcriptome Assembly - Geoduck Tissue-specific Assembly Juvenile Super Low OA EPI116 with HiSeq and NovaSeq Data on Mox

2019
Miscellaneous
Ran a de novo assembly on our HiSeq and NovaSeq data from Hollie’s juvenile EPI 116 sample “super low OA”. This was done for Christian to use in some long, non-coding RNA…
Apr 9, 2019
Sam White
 

Transcriptome Assembly - Geoduck Tissue-specific Assembly Juvenile Super Low OA EPI115 with HiSeq Data on Mox

2019
Miscellaneous
Ran a de novo assembly on our HiSeq data from Hollie’s juvenile EPI 115 sample “super low OA”. This was done for Christian to use in some long, non-coding RNA (lncRNA)…
Apr 9, 2019
Sam White
 

Transcriptome Assembly - Geoduck Tissue-specific Assembly Ctenidia with HiSeq and NovaSeq Data on Mox

2019
Miscellaneous
I previously assembled and annotated P.generosa ctenidia transcriptome (20190318) using just our HiSeq data from our Illumina collaboration. This was a an oversight, as I…
Apr 9, 2019
Sam White
 

Data Management - Whole Genome Bisulfite Sequencing Data from Genewiz Received

2019
Miscellaneous
Received the WGBS data from Genewiz that were sent to Genewiz for whole genome bisulfite sequencing on 20190207. These were from:
Apr 8, 2019
Sam White
 

Metagenomics - P.generosa Water Sample Assembly Comparisons with Quast

2019
Miscellaneous
Continuing work on the metagenomics project, Emma shared her “co-assembly”, so I figured it would be quick and easy to compare hers with mine and get a feel for how…
Apr 8, 2019
Sam White
 

Metagenomics - Geoduck Water Sample Assembly Comparisons with MetaQuast

2019
Miscellaneous
As part of addressing this GitHub Issue on assessing taxonomic diversity in our metagenomics samples, I decided to compare the individual sample assemblies I made on…
Apr 3, 2019
Sam White
 

Metagenomics - Taxonomic Diversity Comparisons from Geoduck Water with Anvio on Mox

2019
Miscellaneous
I decided to give Anvi’o a shot for this metagenomics analysis, as it seems ridiculously thorough and easy to use, with a nice-looking, interactive plotting interface.…
Apr 1, 2019
Sam White
 

Metagenome Assemblies - P.generosa Water Samples Trimmed HiSeqX Data Using Megahit on Mox

2019
Miscellaneous
I previously created a single metagenome assembly using all of the sequencing data from this project.
Mar 27, 2019
Sam White
 

Transposable Element Mapping - Crassostrea gigas Genome v9 Using RepeatMasker 4.07 on Roadrunner

2019
Miscellaneous
Per this GitHub issue, I’m IDing transposable elements (TEs) in the Crassostrea gigas genome. Even though the C.gigas genome should be fully annotated, Steven wants a…
Mar 27, 2019
Sam White
 

Sample Submission - Lotterhos C.virginica Mantle MBD DNA to ZymoResearch for BSseq

2019
Miscellaneous
Crassostrea virginica samples that were subjected to MBD enrichment (completed 20190319) were shipped, on dry ice, to ZymoResearch today for BSseq. They will perform…
Mar 26, 2019
Sam White
 

Data Management - SRA Submission Panopea generosa Day 5 Larvae RNAseq

2019
Miscellaneous
In preparation for some manuscripts, Steven asked that I get some geoduck RNAseq data upload to the NCBI sequencing read archive (SRA) in this GitHub Issue. Specifically, he…
Mar 26, 2019
Sam White
 

Metagenomics - Taxonomic Diversity from Geoduck Water with BLASTn and Krona Plots

2019
Miscellaneous
Continuing on getting the metagenomics sequencing project written up as a manuscript, Steven asked me to provide an overview of the taxonomic makeup of our metagenome…
Mar 25, 2019
Sam White
 

Metagenomics - Taxonomic Diversity from Geoduck Water with BLASTp and Krona plots

2019
Miscellaneous
We’re working on getting the metagenomics sequencing project written up as a manuscript and Steven asked me to provide an overview of the taxonomic makeup of our metagenome…
Mar 25, 2019
Sam White
 

MBD Enrichment - DNA Quantification of C.virginica MBD Samples from 20190312

2019
Miscellaneous
Finished MBD enrichment on 20190312 using the MethylMiner kit. Since we were out of Qubit assay tubes, I could not quantify these samples when I initially completed the…
Mar 19, 2019
Sam White
 

Transcriptome Annotation - Geoduck Juvenile Day 5 with Trinotate on Mox

2019
Miscellaneous
I ran Trinotate (v3.1.1) on Mox to annotate the P.generosa larvae transcriptome I previously assembled with the HiSeq data from Illumina.
Mar 18, 2019
Sam White
 

Transcriptome Annotation - Geoduck Heart with Trinotate on Mox

2019
Miscellaneous
I ran Trinotate (v3.1.1) on Mox to annotate the P.generosa heart transcriptome I previously assembled with the HiSeq data from Illumina.
Mar 18, 2019
Sam White
 

Transcriptome Annotation - Geoduck Ctenidia with Trinotate on Mox

2019
Miscellaneous
I ran Trinotate (v3.1.1) on Mox to annotate the P.generosa ctenidia transcriptome I previously assembled with the HiSeq data from Illumina.
Mar 18, 2019
Sam White
 

Transcriptome Annotation - Geoduck Gonad with Trinotate on Mox

2019
Miscellaneous
I ran Trinotate (v3.1.1) on Mox to annotate the P.generosa gonad transcriptome I previously assembled with the HiSeq data from Illumina.
Mar 18, 2019
Sam White
 

Transcriptome Annotation - Geoduck Heart with BLASTx on Mox

2019
Miscellaneous
I’ll be annotating the transcriptome assembly (from 20190215) using Trinotate and part of that process is having BLASTx output for the Trinity assembly, so have run BLASTx…
Mar 18, 2019
Sam White
 

Transcriptome Annotation - Geoduck Gonad with BLASTx on Mox

2019
Miscellaneous
I’ll be annotating the transcriptome assembly (from 20190215) using Trinotate and part of that process is having BLASTx output for the Trinity assembly, so have run BLASTx…
Mar 18, 2019
Sam White
 

Transcriptome Annotation - Geoduck Ctenidia with BLASTx on Mox

2019
Miscellaneous
I’ll be annotating the transcriptome assembly (from 20190215) using Trinotate and part of that process is having BLASTx output for the Trinity assembly, so have run BLASTx…
Mar 18, 2019
Sam White
 

Transcriptome Annotation - Geoduck Juvenile Day 5 with BLASTx on Mox

2019
Miscellaneous
I’ll be annotating the transcriptome assembly (from 20190215) using Trinotate and part of that process is having BLASTx output for the Trinity assembly, so have run BLASTx…
Mar 18, 2019
Sam White
 

Transcriptome Annotation - Geoduck Juvenile Day 5 with Transdecoder on Mox

2019
Miscellaneous
Continuing tissue-specific RNAseq. Using Transdecoder to identify open reading frames (ORFs). Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Mar 18, 2019
Sam White
 

Transcriptome Annotation - Geoduck Gonad with Transdecoder on Mox

2019
Miscellaneous
Continuing tissue-specific RNAseq. Using Transdecoder to identify open reading frames (ORFs). Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Mar 18, 2019
Sam White
 

Transcriptome Annotation - Geoduck Heart with Transdecoder on Mox

2019
Miscellaneous
Continuing tissue-specific RNAseq. Using Transdecoder to identify open reading frames (ORFs). Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Mar 18, 2019
Sam White
 

Transcriptome Annotation - Geoduck Ctenidia with Transdecoder on Mox

2019
Miscellaneous
Continuing tissue-specific RNAseq. Using Transdecoder to identify open reading frames (ORFs). Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Mar 18, 2019
Sam White
 

Methylation Analysis - C.virginica Gonad MBD with Varying Read Subsets with Bismark on Mox

2019
Miscellaneous
Steven asked for the following analysis in this GitHub Issue using Yaamini’s C.virginica MBD samples:
Mar 13, 2019
Sam White
 

Data Management - Create C.virginica Bisulfite Genome with Bismark on Mox

2019
Miscellaneous
In preparation for some a bisulfite analysis requested by Steven, I needed to make bisulfite genome with, and for, Bismark to use and wanted to use the same one Yaamini has…
Mar 12, 2019
Sam White
 

MBD Enrichment - Ethanol Precipitation of C.virginica MBD samples

2019
Miscellaneous
After completing two rounds of MBD enrichment (first 12 samples on 20190307 and the second 12 samples on 20190311), I performed ethanol precipitation, per the MethylMiner…
Mar 12, 2019
Sam White
 

MBD Enrichment - C.virginica Sheared Mantle DNA from 20190306

2019
Miscellaneous
Last week I performed MBD enrichment on 12 of the 24 Lotterhos C.viriginica mantle DNA on samples I had sheared on 20190306. I proceeded with MBD enrichment using the…
Mar 11, 2019
Sam White
 

MBD Enrichment - C.virginica Sheared Mantle DNA from 20190306

2019
Miscellaneous
Yesterday, I sheared the Lotterhos C.virginica gDNA in preparation for MBD enrichment. Today, I proceeded with MBD enrichment using the MethylMiner Kit (Invitrogen) on 12 of…
Mar 7, 2019
Sam White
 

DNA Shearing & Bioanalyzer - Lotterhos C.virginica Mantle gDNA from 2018114

2019
Miscellaneous
Crassostrea virginica mantle gDNA that had previously been isolated on 20181114 was evaluated for integrity via agaroase gel yesterday (20190305). Everything looked pretty…
Mar 6, 2019
Sam White
 

Agarose Gel - Lotterhos C.virginica Mantle DNA from 20181114

2019
Miscellaneous
Checked DNA integrity of the Crassostrea virginica mantle gDNA I isolated on 20181114 in preparation for MBD enrichment. Detailed sample info and sample processing…
Mar 5, 2019
Sam White
 

Data Management - Data Migration and Drive Expansion on Gannet

2019
Miscellaneous
A little while ago, we installed some additional hard drives in Gannet (Synology RS3618XS) with the intention of expanding the total storage space. However, the original set…
Mar 4, 2019
Sam White
 

Genome Assessment - BUSCO Metazoa on P.generosa v071 on Mox

2019
Miscellaneous
Ran BUSCO on our completed annotation of the P.generosa v071 genome (GFF) (subset of sequences >10kbp). See this notebook entry for genome annotation info. This provides a…
Mar 2, 2019
Sam White
 

Genome Annotation - Pgenerosa_v070 MAKER on Mox

2019
Geoduck Genome Sequencing
Here it goes, a massive undertaking of attempting to annotate the Pgenerosa_v070 genome (FastA; 2.1GB) using MAKER on Mox! I previously started this on 20190115, but killed…
Feb 28, 2019
Sam White
 

Data Wrangling - CpG OE Calculations on C.virginica Genes

2019
Miscellaneous
Steven tasked me with processing ~90 FastA files containing gene sequences from C.virginica in this GitHub Issue. He needed to determine the Observed/Expected (O/E) ratio of…
Feb 26, 2019
Sam White
 

Methylation Analysis - O.lurida Bismark on Mox

2019
Miscellaneous
This is a quick and dirty (i.e. no adaptor/quality trimming) assessment of all of our Ostrea lurida bisulfite sequencing efforts to date in order to get a rough idea of the…
Feb 22, 2019
Sam White
 

Methylation Analysis - P.generosa Bismark on Mox

2019
Miscellaneous
This is a quick and dirty (i.e. no adaptor/quality trimming) assessment of all of our Panopea generosa bisulfite sequencing efforts to date in order to get a rough idea of…
Feb 22, 2019
Sam White
 

Methylation Analysis - C.virginica

2019
Miscellaneous
This is a quick and dirty (i.e. no adaptor/quality trimming) assessment of all of our Crassostrea irginica bisulfite sequencing efforts to date in order to get a rough idea…
Feb 22, 2019
Sam White
 

Methylation Analysis - C.gigas Bismark on Mox

2019
Miscellaneous
This is a quick and dirty (i.e. no adaptor/quality trimming) assessment of all of our Crassostrea gigas bisulfite sequencing efforts to date in order to get a rough idea of…
Feb 22, 2019
Sam White
 

Data Management - Create C.virginica Bisulfite Genome with Bismark on Mox

2019
Crassostrea virginica
eastern oyster
mox
bismark
In preparation for some a quick and “dirty” bisulfite analysis, I needed to make bisulfite genomes with, and for, Bismark to use.
Feb 21, 2019
Sam White
 

Data Management - Create C.gigas Bisulfite Genome with Bismark on Mox

2019
Miscellaneous
In preparation for some a quick and “dirty” bisulfite analysis, I needed to make bisulfite genomes with, and for, Bismark to use.
Feb 21, 2019
Sam White
 

Data Management - Create Geoduck Bisulfite Genomes with Bismark on Mox

2019
Miscellaneous
In preparation for some a quick and “dirty” bisulfite analysis, I needed to make bisulfite genomes with, and for, Bismark to use.
Feb 21, 2019
Sam White
 

Transcriptome Assembly - Geoduck Tissue-specific Assembly Juvenile Day 5

2019
Miscellaneous
Based on a discussion in this GitHub Issue, I’ve initiated some tissue-specific transcriptome assemblies with our current geoduck data.
Feb 15, 2019
Sam White
 

Transcriptome Assembly - Geoduck Tissue-specific Assembly Heart

2019
Miscellaneous
Based on a discussion in this GitHub Issue, I’ve initiated some tissue-specific transcriptome assemblies with our current geoduck data.
Feb 15, 2019
Sam White
 

Transcriptome Assembly - Geoduck Tissue-specific Assembly Gonad

2019
Miscellaneous
Based on a discussion in this GitHub Issue, I’ve initiated some tissue-specific transcriptome assemblies with our current geoduck data.
Feb 15, 2019
Sam White
 

Transcriptome Assembly - Geoduck Tissue-specific Assembly Ctenidia

2019
Miscellaneous
Based on a discussion in this GitHub Issue, I’ve initiated some tissue-specific transcriptome assemblies with our current geoduck data.
Feb 15, 2019
Sam White
 

Genome Annotation - Pgenerosa_v71 with MAKER on Mox

2019
Miscellaneous
With the P.generosa v070 annotation taking a very long time (due to the genome/transcriptome sizes, and, hitting some snags in the script I put together), Steven asked if I…
Feb 13, 2019
Sam White
 

Sequence Subsetting - Pgenerosa_v70 Genome Assembly with faidx

2019
Miscellaneous
Steven asked to subset geoduck assembly in to >10kbp and >30kbp groups. Here are the commands, using faidx:
Feb 11, 2019
Sam White
 

Samples Submitted - Robertos C.gigas DNA for Whole Genome Bisulfite Sequencing (Genewiz)

2019
Samples Submitted
Sent Roberto’s 12 designated DNA samples for whole genome bisulfite sequencing (WGBS) to Genewiz. They will do all bisulfite conversion, library prep and sequencing…
Feb 7, 2019
Sam White
 

Samples Received - C.virginica DNA and Tissues from Lotterhos Lab

2019
Samples Received
Sample list is here (Google Sheet):
Jan 29, 2019
Sam White
 

DNA Isolation and Quantification - Ronit's C.gigas Ploidy Ctenidia

2019
Miscellaneous
Last week, I isolated DNA from all of Ronti’s ctenidia samples, however one sample (D18-C) didn’t isolate properly. So, I performed another isolation procedure with another…
Jan 23, 2019
Sam White
 

DNA Isolation - C.gigas Ploidy Experiment Ctenidia

2019
Miscellaneous
Isolated DNA from the remaining ctenidia tissue samples from Ronit’s experiment (Google Sheet).
Jan 17, 2019
Sam White
 

Annotation - Olurida_v081 MAKER BUSCO Metazoa Augustus Training on Mox

2019
Olympia Oyster Genome Sequencing
Previously performed this analysis using the eukaryota_odb9 BUSCO database. Figured I’d give it another go using a more specific database, metazoa_odb9, for comparison.
Jan 15, 2019
Sam White
 

Annotation - Geoduck Genome with MAKER Submitted to Mox

2019
Geoduck Genome Sequencing
Well, here we go! Initiating full-blown annotation of the Pgenerosa_v070 (FastA; 2.1GB), using MAKER (v.2.31.10) on Mox. This will perform the following:
Jan 15, 2019
Sam White
 

Annotation - Olurida_v081 MAKER BUSCO (eukaryota_odb9) Augustus Training Submitted to Mox

2019
Olympia Oyster Genome Sequencing
I’ve previously run MAKER, followed by two round of SNAP gene predictions and now I’m going to throw a BUSCO/Augustus gene training & prediction in the mix to see how it…
Jan 14, 2019
Sam White
 

Annotation - Olurida_v081 MAKER Functional Annotations on Mox

2019
Olympia Oyster Genome Sequencing
Believe it or not, full, proper annotation of the Olympia oyster genome is nearly complete! Here’s where it stands:
Jan 9, 2019
Sam White
 

Annotation - Olurida_v081 MAKER Proteins BLASTp on Mox

2019
Olympia Oyster Genome Sequencing
After getting through the initial MAKER annotation and SNAP gene predictions, and then renaming the sequences, I needed to run BLASTp on the FastA file produced by MAKER id…
Jan 8, 2019
Sam White
 

Annotation - Olurida_v081 MAKER Proteins InterProScan5 on Mox

2019
Olympia Oyster Genome Sequencing
Continuation of genome annotation of the Olympia oyster genome. Determined initial gene models using MAKER with two rounds of SNAP, relabeled with more user-friendly names…
Jan 8, 2019
Sam White
 

Annotation - Olurida_v081 MAKER ID Mapping

2019
Olympia Oyster Genome Sequencing
After getting through the initial MAKER annotation and SNAP gene predictions, I needed (wanted?) to simplify annotation names that will be easier to read and are in a more…
Jan 8, 2019
Sam White
 

Gene Prediction - HiSeqX Metagenomics from Geoduck Water Using MetaGeneMark on Mox

2019
Miscellaneous
After assembline the metagenomic data yesterday, I needed to predict some genes. I did this using MetaGeneMark (v.3.38) and ran it on Mox.
Jan 3, 2019
Sam White
 

Metagenome Assembly - P.generosa Water Sample Trimmed HiSeqX Data Using Megahit on Mox

Panopea generosa
geoduck
megahit
mox
metagenome
assembly
2019
Miscellaneous
Attempting an assembly of our geoduck metagenomics HiSeqX data using Megahit (v.1.1.4) on a Mox node.
Jan 2, 2019
Sam White
 

VCF Splitting - C.virginica VCF Using BCFtools

2019
Miscellaneous
Steven asked that I split up a Crassostrea virginica VCF file:
Jan 2, 2019
Sam White
 

DNA Isolation - C.gigas Ploidy Experiment Ctenidia

2018
Miscellaneous
Yesterday, Ronit initiated DNA isolation from ctenidia samples from his experiment (Google Sheet) from the following four samples:
Dec 20, 2018
Sam White
 

Repeat Library Construction - P.generosa RepeatModeler v1.0.11

emu
repeatmodeler
jupyter notebook
Panopea generosa
geoduck
Pgenerosa_v070.fa
2018
Geoduck Genome Sequencing
Needed to generate a generate a species-specific repeat library for use with MAKER genome annotation using RepeatModeler and the Pgenerosa_v070.fa (see our Genomic Resources…
Dec 19, 2018
Sam White
 

qPCR - Relative mitochondrial abundance in C.gigas diploids and triploids subjected to acute heat stress via COX1

qPCR
Crassostrea gigas
Pacific oyster
CFX Connect
SsoFast EVAGreen
COX1
2018
Miscellaneous
Using the C.gigas cytochrome c oxidase (COX1) primers (SR IDs: 1713, 1714)I designed the other day, I ran a qPCR on a subset of Ronit’s diploid/triploid control/heat shocked…
Dec 17, 2018
Sam White
 

BLASTx - Clupea pallasii (Pacific herring) liver and testes transcriptomes on Mox

2018
Miscellaneous
Apparently we’ve had some interest in the Pacific herring transcriptomes (liver and testes) we produced many years ago. As such, Steven asked that I do a quick BLASTx to…
Dec 12, 2018
Sam White
 

FastQC and Trimming - Metagenomics (Geoduck) HiSeqX Reads from 20180809

2018
Miscellaneous
Steven tasked me with assembling our geoduck metagenomics HiSeqX data. The first part of the process is examining the quality of the sequencing reads, performing quality…
Dec 11, 2018
Sam White
 

Primer Design - Gigas COX1 using Primer3

2018
Miscellaneous
We’re attempting a quick & dirty comparison of relative mitochondria counts between diploid and triploid C.gigas, so needed a single-copy mitochondrial gene target for qPCR.…
Dec 11, 2018
Sam White
 

qPCR - Geoduck gonad cDNA with vitellogenin primers

qPCR
CFX
2x SsoFast EVAgreen
geoduck
vtg
vitellogenin
Panopea generosa
gonad
2018
Earlier today I made some cDNA from geoduck gonad RNA for use in this qPCR to test out the vitellogenin primers I designed on 20181129
Dec 6, 2018
Sam White
 

Reverse Transcription - Geoduck gonad RNA pool

2018
Miscellaneous
To be able to actually test the vitellegenin primers I made, I needed some geoduck cDNA.
Dec 6, 2018
Sam White
 

Primer Design - Geoduck Vitellogenin using Primer3

2018
Miscellaneous
In preparation for designing primers for developing a geoduck vitellogenin qPCR assay, I annotated a de novo geoduck transcriptome assembly last week. Next up, identify…
Nov 29, 2018
Sam White
 

Annotation - Olurida_v081 MAKER on Mox

Ostrea lurida
Olympia oyster
mox
MAKER
genome annotation
Olurida_v081
2018
Olympia Oyster Genome Sequencing
Remarkably, I managed to burn through our Xsede computing resources and don’t have terribly much to show for it. Ooof! This is a major bummer, as it “only” takes ~8hrs for a…
Nov 27, 2018
Sam White
 

Annotation - Geoduck Transcritpome with TransDecoder

TransDecoder
geoduck
Panopea generosa
annotation
transcriptome
mox
2018
I was tasked with generating some qPCR primers to analyze vitellogenin expression in geoduck. In order to do so, I needed to annotate a geoduck transcriptome in order to…
Nov 21, 2018
Sam White
 

RNA Quantification - Ronit's C.gigas DNased RNA from 20181115

RNA quantification
Qubit 3.0
Qubit hsRNA
Crassostrea gigas
pacific oyster
diploid
triploid
dessication
DNased RNA
2018
After confirming Ronit’s DNased RNA was free of gDNA, I quantified the DNased RNA from 20181115 using the Roberts Lab Qubit 3.0 and the Qubit hsRNA Assay.
Nov 20, 2018
Sam White
 

Reverse Transcription - Ronit's C.gigas DNased RNA from 20181115

reverse transcription
cDNA
MMLV
pacific oyster
Crassostrea gigas
diploid
triploid
dessication
2018
Quantified Ronit’s DNased RNA earlier today and proceeded with reverse transcription using 100ng of DNased RNA with oligo dT primers (Promega) and M-MLV reverse…
Nov 20, 2018
Sam White
 

DNase - Ronit's C.gigas Ctenidia RNA

2018
Miscellaneous
Ronit finished his RNA isolations for his ctenidia samples on 20181025 & 20181101, as well as quntification (he has no notebook entry for this, at this time). However, his…
Nov 15, 2018
Sam White
 

qPCR - Ronit's DNased C.gigas RNA with Elongation Factor Primers

2018
Miscellaneous
After DNasing Ronit’s RNA earlier today, I needed to verify the RNA was free of any contaminating gDNA.
Nov 15, 2018
Sam White
 

DNA Isolation and Quantification - Lotterhos C.virginica Mantle DNA

2018
Miscellaneous
Isolated DNA from the Lotterhos Crassostrea virginica mantle samples received on 20181017 using the E.Z.N.A. Mollusc Kit, with the following modifications/notes:
Nov 14, 2018
Sam White
 

Computing - Install NCBI nr nt BLAST Database on Mox

2018
Miscellaneous
Per this issue on GitHub, I installed the pre-formatted NCBI non-redudant (nr) nucleotide (nt) database on Mox.
Nov 14, 2018
Sam White
 

My New Notebook

computing
wordpress
jekyll
onsnetwork
2018
Here we are - my new notebook!
Nov 8, 2018
Sam White
 

Repeat Library Construction - O.lurida RepeatModeler v1.0.11

emu
repeatmodeler
jupyter notebook
Ostrea lurida
olympia oyster
2018
Olympia Oyster Genome Sequencing
In further attempts to improve our Ostrea lurida genome annotation, I decided to generate a species-specific repeat library for use with MAKER genome annotation using RepeatM…
Oct 22, 2018
Sam White
 

qPCRs - Ronit's C.gigas ploidy/dessication/heat stress cDNA (1:5 dilution)

2018
Miscellaneous
IMPORTANT: The cDNA used for the qPCRs described below was a 1:5 dilution of Ronit’s cDNA made 20181017 with the following primers! Diluted cDNA was stored in his -20oC box…
Oct 18, 2018
Sam White
 

Samples Received - Crassostrea virginica (Eastern oyster) tissue from Lotterhos Lab (Northeastern University)

2018
Samples Received
Sample sheet (Google Sheet):
Oct 17, 2018
Sam White
 

Reverse Transcription - Ronit's C.gigas DNased ctenidia RNA

2018
Miscellaneous
Proceeded with reverse transcription of [Ronit’s DNased ctenidia RNA (from 20181016)(2018-10-16-dnase-treatment-ronits-c-gigas-ploiyddessication-ctenidia-rna.html).
Oct 17, 2018
Sam White
 

qPCR - Ronit’s DNAsed C.gigas Ploidy/Dessication RNA with elongation factor primers

2018
Miscellaneous
After I figured out the appropriate DNA and primers to use to detect gDNA in Crassostrea gigas samples, I checked Ronit’s [DNased ctenidia RNA (from…
Oct 17, 2018
Sam White
 

qPCR – C.gigas primer and gDNA tests with 18s and EF1 primers

2018
BB15
BB16
cfx connect
Cg_18s_1644_F
Cg_18s_1750_R
Crassostrea gigas
EF1_qPCR_3'
EF1_qPCR_5'
Pacific oyster
qPCR
SRID 1168
SRID 1169
SRID 309
SRID 310
SsoFast EvaGreen Supermix
The qPCR I ran earlier today to check for residual gDNA in Ronit’s DNased RNA turned out terribly, due to a combination of bad primers and, possibly, bad gDNA.
Oct 16, 2018
Sam White
 

qPCR - Ronit's DNAsed C.gigas Ploidy/Dessication RNA with 18s primers

2018
Miscellaneous
After DNasing Ronit’s RNA earlier today, I needed to check for any residual gDNA.
Oct 16, 2018
Sam White
 

DNase Treatment - Ronit's C.gigas Ploiyd/Dessication Ctenidia RNA

2018
Miscellaneous
After quantifying Ronit’s RNA earlier today, I DNased them using the Turbo DNA-free Kit (Ambion), according to the manufacturer’s standard protocol.
Oct 16, 2018
Sam White
 

RNA Quantification - Ronit's C.gigas Ploidy/Dessication RNA

2018
Miscellaneous
Last Friday, Ronit quantified 1:10 dilutions of the RNA I isolated on 20181003 and the RNA he finished isolating on 20181011, but two of the samples (D11-C, T10-C) were…
Oct 16, 2018
Sam White
 

Data Received - Chionoecetes bairdi RNAseq & FastQC Analysis

2018
Miscellaneous
We received Grace’s 100bp PE NovaSeq (Illumian) RNAseq data from the Northwest Genomics Center today.
Oct 15, 2018
Sam White
 

VCF Splitting with bcftools

2018
Miscellaneous
Steven asked for some help trying to split a VCF in to individual VCF files.
Oct 15, 2018
Sam White
 

RNA Isolation - Tanner Crab Hemolymph Pellet in RNAlater using TriReagent

2018
Chionoecetes bairdi
Qubit 3.0
Qubit RNA HS
RNA
RNA isolation
RNA quantification
tanner crab
TriReagent
I previously isolated RNA from crab hemolymp from a lyophilized sample using TriReagent and Grace recently tried isolating RNA from crab hemolyph pellet (non-lyophilized)…
Oct 9, 2018
Sam White
 

RNA Isolation - Ronit's C.gigas diploid/triploid dessication/heat shock ctenidia tissues

2018
Miscellaneous
Isolated RNA from a subset of Ronit’s Crassostrea gigas ctenidia samples (see Ronit’s notebook for experiment deets):
Oct 3, 2018
Sam White
 

SRA Submission - Olymia oyster Whole Genome BS-seq Data

2018
Olympia oyster reciprocal transplant
Submitted our whole genome bisulfite sequencing data to NCBI Sequence Read Archive (SRA).
Oct 3, 2018
Sam White
 

Installation - Microsoft Machine Learning Server (Microsoft R Open) on Emu/Roadrunner R Studio Server

2018
Miscellaneous
Steven recently saw an announcement that Microsoft R Open now handles multi-threaded processing (default R does not), so we were interested in trying it out. I installed…
Oct 2, 2018
Sam White
 

Ubuntu – Fix “No Video Signal” Issue on Emu

2018
Computer Servicing
An issue with Emu cropped up a few weeks ago that was seemingly caused by upgrading from Ubuntu 16.04 to 18.04.
Oct 2, 2018
Sam White

Transcriptome Alignment & Bedgraph – Olympia oyster transcriptome with Olurida_v080 genome assembly

2018
Miscellaneous
Yesterday, I produced a bedgraph file of our Olympia oyster RNAseq data coverage using our Olurida_v081 genome.
Sep 26, 2018
Sam White

Bedgraph – Olympia oyster transcriptome with Olurida_v081 genome assembly

2018
Miscellaneous
I took the sorted BAM file from yesterday’s corrected RNAseq genome alignment and converted it to a bedgraph using BEDTools genomeCoverageBed tool.
Sep 26, 2018
Sam White
 

Transcriptome Alignment – Olympia oyster RNAseq reads aligned to genome with HISAT2

2018
Miscellaneous
Yesterday’s attempt at producing a bedgraph was a failure and a prodcuct of a major brain fart. The worst part is that I was questioning what I was doing the entire time…
Sep 25, 2018
Sam White
 

Bedgraph - Olympia oyster transcriptome (FAIL)

2018
Miscellaneous
Progress on generating bedgraphs from our Olympia oyster transcriptome continues.
Sep 24, 2018
Sam White
 

Transcriptome Alignment - Olympia oyster Trinity transcriptome aligned to genome with Bowtie2

2018
Miscellaneous
Progress on generating bedgraphs from our Olympia oyster transcriptome continues.
Sep 19, 2018
Sam White
 

Transcriptome Assembly - Olympia oyster RNAseq Data with Trinity

2018
Miscellaneous
Used all of our current oly RNAseq data to assemble a transcriptome using Trinity.
Sep 19, 2018
Sam White
 

DNA Methylation Analysis – Olympia Oyster Whole Genome BSseq Bismark Pipeline MethylKit Comparison

2018
Miscellaneous
I previously ran two variations on the Bismark analysis for our Olympia oyster whole genome bisulfite sequencing data:
Sep 18, 2018
Sam White
 

RNA Isolation - Lyophilized Tanner Crab Hemolymph in RNAlater

2018
Miscellaneous
Due to difficulties getting RNA from hemolymph samples stored in RNAlater, Grace is testing out lyophilizing samples before extraction. Who knows what impact this will have…
Sep 17, 2018
Sam White
 

DNA Methylation Analysis - Olympia Oyster Whole Genome BSseq Bismark Pipeline Comparison

2018
Miscellaneous
Ran Bismark using our high performance computing (HPC) node, Mox, with two different bowtie2 settings:
Sep 13, 2018
Sam White
 

DNA Quantification - Sea Lice DNA from 20180523

2018
Miscellaneous
We previously received sea lice (Caligus tape) DNA from Cris Gallardo-Escarate at Universidad de Concepción.
Sep 12, 2018
Sam White
 

TrimGalore/FastQC/MultiQC - C.virginica Oil Spill MBDseq Concatenated Sequences

2018
LSU C.virginica Oil Spill MBD BS Sequencing
Previously concatenated and analyzed our Crassostrea virginica oil spill MBDseq data with FastQC.
Sep 11, 2018
Sam White
 

Sequencing Data Analysis - C.virginica Oil Spill MBDseq Concatenation & FastQC

2018
LSU C.virginica Oil Spill MBD BS Sequencing
Per Steven’s request, I concatenated our Crassostrea virginica LSU oil spill MBDseq sequencing data and ran FastQC on the concatenated files.
Sep 10, 2018
Sam White
 

DNA Methylation Analysis - Olympia oyster BSseq MethylKit Analysis

2018
bismark
BSseq
methylation
methylkit
Olympia oyster
Ostrea lurida
The goal of this analysis was to compare the methylation profiles of Olympia oysters originating from a common population (Fidalgo Bay) that were raised in two different…
Sep 4, 2018
Sam White
 

Transcriptome Assembly - Geoduck RNAseq data

2018
Miscellaneous
Used all of our current geoduck RNAseq data to assemble a transcriptome using Trinity.
Sep 4, 2018
Sam White
 

FastQC/MultiQC/TrimGalore/MultiQC/FastQC/MultiQC - O.lurida WGBSseq for Methylation Analysis

2018
BSseq
FASTQC
mox
multiqc
olympia oyster
Ostrea lurida
TrimGalore!
trimming
I previously ran this data through the Bismark pipeline and followed up with MethylKit analysis. MethylKit analysis revealed an extremely low number of differentially…
Aug 30, 2018
Sam White
 

Transposable Element Mapping – Crassostrea virginica Genome, Cvirginica_v300, using RepeatMasker 4.07

2018
Miscellaneous
Per this GitHub issue, I’m IDing transposable elements (TEs) in the Crassostrea virginica genome.
Aug 28, 2018
Sam White
 

Assembly Stats – Geoduck Hi-C Final Assembly Comparison

2018
Geoduck Genome Sequencing
We received the final geoduck genome assembly data from Phase Genomics, in which they updated the assembly by performing some manual curation:
Aug 23, 2018
Sam White
 

DNA Methylation Analysis - Bismark Pipeline on All Olympia oyster BSseq Datasets

2018
Miscellaneous
Bismark analysis of all of our current Olympia oyster (Ostrea lurida) DNA methylation high-throughput sequencing data.
Aug 16, 2018
Sam White
 

Data Received - Geoduck Metagenome HiSeqX Data

2018
Miscellaneous
FastQ files are being transferred to owl/nightingales/P_generosa.
Aug 9, 2018
Sam White
 

RNA Isolation & Quantificaiton - Tanner Crab Hemolymph

2018
Miscellaneous
Isolated RNA from 40 Tanner crab hemolymph samples selected by Grace with the RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s protocol, with the following…
Aug 9, 2018
Sam White
 

Genome Annotation – Olympia oyster genome annotation results #02

2018
Olympia Oyster Genome Sequencing
Yesterday, I annotated our Olympia oyster genome using WQ-MAKER in just 7hrs!.
Aug 8, 2018
Sam White
 

Genome Annotation - Olympia oyster genome annotation results #01

2018
Olympia Oyster Genome Sequencing
Yesterday, I annotated our Olympia oyster genome using WQ-MAKER in just 7hrs!.
Aug 8, 2018
Sam White
 

Genome Annotation – Olympia oyster genome complete - brief note

2018
Olympia Oyster Genome Sequencing
Whoa! Genome annotation using Jetstream/WQ-MAKER that I started this morning is complete!! Only 7hrs!
Aug 7, 2018
Sam White
 

Genome Annotation - Olympia oyster genome using WQ-MAKER Instance on Jetstream

2018
Olympia Oyster Genome Sequencing
annotation
Atmosphere
Cyverse
genome
JetStream
maker
olympia oyster
Ostrea lurida
wq-maker
Xsede
Yesterday, our Xsede Startup Application (Google Doc) got approval for 100,000 Service Units (SUs) and 1TB of disk space on Xsede/Atmosphere/Jetstream (or, whatever it’s…
Aug 7, 2018
Sam White
 

Bioanalyzer - Tanner Crab RNA Isolated with RNeasy Plus Mini Kit

2018
Miscellaneous
Ran the four Tanner crab RNA samples that I isolated yesterday on the Seeb Lab Bioanalyzer 2100 (Agilent) using the RNA Pico 6000 Kit.
Aug 1, 2018
Sam White
 

RNA Cleanup - Tanner Crab RNA

2018
Miscellaneous
In a continued attempt to figure out what we can do about the tanner crab RNA, Steven tasked me with using an RNeasy Kit to cleanup some existing RNA.
Jul 31, 2018
Sam White
 

RNA Isolation - Tanner Crab Hemolymph Using RNeasy Plus Mini Kit

2018
Miscellaneous
Tanner crab RNA has proved a bit troublesome. As such, [Steven asked me to try isolating some RNA using the RNeasy Plus Mini Kit…
Jul 31, 2018
Sam White
 

Mox – Over quota: Olympia oyster genome annotation progress (using Maker 2.31.10)

2018
Olympia Oyster Genome Sequencing
Per this GitHub Issue, Steven has cleared out files.
Jul 30, 2018
Sam White
 

RNA Cleanup - Tanner Crab RNA Pools

2018
Tanner Crab RNAseq
Grace had previously pooled a set of crab RNA in preparation for RNAseq. Yesterday, we/she concentrated the samples and then quantified them. Unfortunately, Qubit results…
Jul 19, 2018
Sam White
 

Mox - Olympia oyster genome annotation progress (using Maker 2.31.10)

2018
Olympia Oyster Genome Sequencing
I decided to spend some time to figure out what was actually happening, as it’s clear that the annotation process is going to need some additional time to run and may span…
Jul 11, 2018
Sam White
 

Mox - Password-less SSH!

2018
Miscellaneous
The high performance computing (HPC) cluster (called Mox) at Univ. of Washington (UW) frustratingly requires a password when SSH-ing, even when SSH keys are in use. I have a…
Jul 11, 2018
Sam White
 

Ubuntu - Fix "No Video Signal" Issue on Emu/Roadrunner

2018
Computer Servicing
Both Apple Xserves (Emu/Roadrunner) running Ubuntu (16.04LTS) experienced the same issue - the monitor would indicate “No Video Signal”, would go dark, and wasn’t responsive…
Jul 5, 2018
Sam White
 

Transposable Element Mapping – Olympia Oyster Genome Assembly, Olurida_v081, using RepeatMasker 4.07

2018
Miscellaneous
I previously performed this analysis using a different version of our Ostrea lurida genome assembly. Steven asked that I repeat the analysis with a modified version of the…
Jul 3, 2018
Sam White
 

Library Construction - Geoduck Water Filter Metagenome with Nextera DNA Flex Kit (Illumina)

2018
bioanalyzer
geoduck
library prep
metagenomics
nextera
Panopea generosa
Qubit 1x dsDNA HS Assay Kit
Qubit 3.0
Made Illumina libraries with goeduck metagenome water filter DNA I previously isolated on:
Jun 6, 2018
Sam White
 

BS-seq Mapping – Olympia oyster bisulfite sequencing: Bismark Continued

2018
Miscellaneous
Previously took the analysis just through the mapping, but didn’t realize Steven wanted me to fully process the data.
May 31, 2018
Sam White
 

Transposable Element Mapping – Crassostrea virginica NCBI Genome Assembly using RepeatMasker 4.07

2018
Miscellaneous
Genome used: NCBI GCA_002022765.4_C_virginica-3.0
May 29, 2018
Sam White
 

Read Mapping – Olympia oyster 2bRAD Data with Bowtie2 (on Mox)

2018
Miscellaneous
May 26, 2018
Sam White
 

Transposable Element Mapping - Olympia Oyster Genome Assembly using RepeatMasker 4.07

2018
Miscellaneous
Steven wanted transposable elements (TEs) in the Olympia oyster genome identified.
May 23, 2018
Sam White
 

DNA Received - Sea lice DNA from Cris Gallardo-Escarate at Universidad de Concepción

2018
Samples Received
Received Caligus tape DNA - two samples:
May 23, 2018
Sam White
 

Software Installation – RepeatMasker v4.0.7 on Emu/Roadrunner Continued

2018
Miscellaneous
After yesterday’s difficulties getting RMblast to compile, I deleted the folder and went through the build process again.
May 23, 2018
Sam White
 

Software Installation - RepeatMasker v4.0.7 on Emu/Roadrunner

2018
emu
RepeatMasker
roadrunner
TE
transposable elements
Steven asked that I re-run some Olympia oyster transposable elements analysis using RepeatMasker and a newer version of our Olympia oyster genome assembly.
May 22, 2018
Sam White
 

TrimGalore/FastQC/MultiQC – TrimGalore! RRBS Geoduck BS-seq FASTQ data (directional)

2018
Miscellaneous
Earlier this week, I ran TrimGalore!, but set the trimming, incorrectly - due to a copy/paste mistake, as --non-directional, so I re-ran with the correct settings.
May 16, 2018
Sam White
 

FastQC - RRBS Geoduck BS-seq FASTQ data

2018
Miscellaneous
Earlier today I finished trimming Hollie’s RRBS BS-seq FastQ data.
May 16, 2018
Sam White
 

TrimGalore/FastQC/MultiQC – TrimGalore! RRBS Geoduck BS-seq FASTQ data

2018
Miscellaneous
Steven requested that I trim the Geoduck RRBS libraries that we have, in preparation to run them through Bismark.
May 16, 2018
Sam White
 

Data Management - Illumina NovaSeq Geoduck Genome Sequencing

2018
Geoduck Genome Sequencing
As part of the Illumina collaborative geoduck genome sequencing project, their end goal has always been to sequence the genome in a single run.
May 16, 2018
Sam White
 

Assembly - Geoduck Hi-C Assembly Subsetting

2018
Geoduck Genome Sequencing
Steven asked me to create a couple of subsets of our Phase Genomics Hi-C geoduck genome assembly (pga_02):
May 12, 2018
Sam White
 

Read Mapping - Mapping Illumina Data to Geoduck Genome Assemblies with Bowtie2

2018
Geoduck Genome Sequencing
We have an upcoming meeting with Illumina to discuss how the geoduck genome project is coming along and to decide how we want to proceed.
May 9, 2018
Sam White
 

BS-seq Mapping - Olympia oyster bisulfite sequencing: TrimGalore > FastQC > Bismark

2018
BS-seq Libraries for Sequencing at Genewiz
MBD Enrichment for Sequencing at ZymoResearch
Steven asked me to evaluate our methylation sequencing data sets for Olympia oyster.
May 8, 2018
Sam White
 

Assembly & Stats - SparseAssembler (k95) on Geoduck Sequence Data > Quast for Stats

2018
Geoduck Genome Sequencing
Had a successful assembly with SparseAssembler k101, but figured I’d just tweak the kmer setting and throw it in the queue and see how it compares; minimal effort/time needed.
May 1, 2018
Sam White
 

Assembly Stats - Geoduck Genome Assembly Comparisons w/Quast - SparseAssembler, SuperNova, Hi-C

2018
Geoduck Genome Sequencing
Steven requested a comparison of geoduck genome assemblies.
Apr 30, 2018
Sam White
 

Assembly Stats - Geoduck Hi-C Assembly Comparison

2018
Geoduck Genome Sequencing
Ran the following Quast command to compare the two geoduck assemblies provided to us by Phase Genomics:
Apr 30, 2018
Sam White
 

DNA Isolation & Quantification - Metagenomics Water Filters

2018
Miscellaneous
After discussing the preliminary DNA isolation attemp with Steven & Emma, we decided to proceed with DNA isolations on the remaining 0.22μm filters.
Apr 26, 2018
Sam White
 

Total Alkalinity Calculations - Yaamini's Ocean Chemistry Samples

2018
Miscellaneous
I ran a subset of Yaamini’s ocean chemistry samples on our T5 Excellence titrator (Mettler Toledo) at the beginning of April. The subset were samples taken from the…
Apr 24, 2018
Sam White
 

Assembly – SparseAssembler (k 111) on Geoduck Sequence Data

2018
Geoduck Genome Sequencing
Continuing to try to find the best kmer setting to work with SparseAssemlber after the last attempt failed due to a kmer size that was too large (k 131; which happens to be…
Apr 23, 2018
Sam White
 

Assembly – SparseAssembler (k 131) on Geoduck Sequence Data

2018
Geoduck Genome Sequencing
After some runs with kmergenie, I’ve decided to try re-running SparseAssembler using a kmer setting of 131.
Apr 22, 2018
Sam White
 

Data Management - Geoduck Phase Genomics Hi-C Data

2018
Geoduck Genome Sequencing
Samples Received
We received sequencing/assembly data from Phase Genomics.
Apr 21, 2018
Sam White
 

Kmer Estimation – Kmergenie (k 301) on Geoduck Sequence Data

2018
Geoduck Genome Sequencing
Continuing the quest for the ideal kmer size to use for our geoduck assembly.
Apr 21, 2018
Sam White
 

Kmer Estimation – Kmergenie Tweaks on Geoduck Sequence Data

2018
Geoduck Genome Sequencing
geoduck
kmer
kmer genie
mox
Panopea generosa
Earlier today, I ran kmergenie on our all of geoduck DNA sequencing data to see what it would spit out for an ideal kmer setting, which I would then use in another assembly…
Apr 19, 2018
Sam White
 

Kmer Estimation - Kmergenie on Geoduck Sequence Data (default settings)

2018
Geoduck Genome Sequencing
geoduck
kmer
kmer genie
mox
Panopea generosa
After the last SparseAssembler assembly completed, I wanted to do another run with a different kmer size (last time was arbitrarily set at 101). However, I didn’t really…
Apr 19, 2018
Sam White
 

Assembly Stats - Quast Stats for Geoduck SparseAssembler Job from 20180405

2018
Geoduck Genome Sequencing
The geoduck genome assembly started 20180405 completed this weekend.
Apr 15, 2018
Sam White
 

Data Management - SRA Submission LSU C.virginica Oil Spill MBD BS-seq Data

2018
LSU C.virginica Oil Spill MBD BS Sequencing
Submitted the Crassostrea virginica (Eastern oyster) MBD BS-seq data we received on 20150413 to NCBI Sequence Read Archive.
Apr 12, 2018
Sam White
 

TrimGalore/FastQC/MultiQC - Trim 10bp 5'/3' ends C.virginica MBD BS-seq FASTQ data

2018
Crassostrea virginica
Eastern oyster
FASTQC
MBD-Seq
multiqc
TrimGalore!
ZymoResearch
Steven found out that the Bismarck documentation (Bismarck is the bisulfite aligner we use in our BS-seq pipeline) suggests trimming 10bp from both the 5’ and 3’ ends. Since…
Apr 11, 2018
Sam White
 

DNA Isolation & Quantification - Metagenomics Water Filters

2018
Miscellaneous
Isolated DNA from the following two filters:
Apr 11, 2018
Sam White
 

TrimGalore/FastQC/MultiQC - 2bp 3' end Read 1s Trim C.virginica MBD BS-seq FASTQ data

2018
Crassostrea virginica
Eastern oyster
FASTQC
MBD-Seq
multiqc
TrimGalore!
ZymoResearch
Earlier today, I ran TrimGalore/FastQC/MultiQC on the Crassostrea virginica MBD BS-seq data from ZymoResearch and hard trimmed the first 14bp from each read. Things looked…
Apr 10, 2018
Sam White
 

TrimGalore/FastQC/MultiQC - 14bp Trim C.virginica MBD BS-seq FASTQ data

2018
Miscellaneous
Yesterday, I ran TrimGalore/FastQC/MultiQC on the Crassostrea virginica MBD BS-seq data from ZymoResearch with the default settings (i.e. “auto-trim”). There was still some…
Apr 10, 2018
Sam White
 

TrimGalore/FastQC/MultiQC - Auto-trim C.virginica MBD BS-seq FASTQ data

2018
Miscellaneous
Yesterday, I ran FastQC/MultiQC on the Crassostrea virginica MBD BS-seq data from ZymoResearch. Steven wanted to trim it and see how things turned out.
Apr 9, 2018
Sam White
 

FastQC/MultiQC - C. virginica MBD BS-seq Data

2018
Miscellaneous
Per Steven’s GitHub Issues request, I ran FastQC on the Eastern oyster MBD bisulfite sequencing data we recently got back from ZymoResearch.
Apr 9, 2018
Sam White
 

Genome Assembly - SparseAssembler Geoduck Genomic Data, kmer=101

2018
Geoduck Genome Sequencing
Assembly complete. See end of post for data locations.
Apr 5, 2018
Sam White
 

Gunzip - BGI HiSeq Geoduck Genome Sequencing Data

2018
Geoduck Genome Sequencing
In preparation to run SpareAssembler, I needed to gunzip the BGI gzipped FASTQ files from 20180327.
Apr 5, 2018
Sam White
 

Gunzip - Trimmed Illumina Geoduck HiSeq Genome Sequencing Data

2018
Geoduck Genome Sequencing
In preparation to run SpareAssembler, I needed to gunzip the trimmed gzipped FASTQ files from 20140401.
Apr 4, 2018
Sam White
 

DNA Isolation & Quantification – Geoduck larvae metagenome filter rinses

2018
Miscellaneous
This is another attempt to isolate DNA from two more of the geoduck hatchery metagenome samples Emma delivered on 20180313.
Apr 3, 2018
Sam White
 

Titrations - Yaamini's Seawater Samples

2018
Miscellaneous
All data is deposited in the following GitHub repo:
Apr 3, 2018
Sam White
 

Titrations - Yaamini's Seawater Samples

2018
Miscellaneous
All data is deposited in the following GitHub repo:
Apr 2, 2018
Sam White
 

TrimGalore!/FastQC/MultiQC - Illumina HiSeq Genome Sequencing Data Continued

2018
Geoduck Genome Sequencing
The previous attempt at this was interrupted by a random glitch with our Mox HPC node.
Apr 1, 2018
Sam White
 

Data Received - Crassostrea virginica MBD BS-seq from ZymoResearch

2018
Miscellaneous
Received the sequencing data from ZymoResearch for the Crassostrea virginica gonad MBD DNA that was sent to them on 20180207 for bisulfite conversion, library construction…
Mar 29, 2018
Sam White
 

FastQC/MultiQC – Illumina HiSeq Genome Sequencing Data

2018
Geoduck Genome Sequencing
Since running SparseAssembler seems to be working and actually able to produce assemblies, I’ve decided I’ll try to beef up the geoduck genome assembly with the rest of our…
Mar 28, 2018
Sam White
 

TrimGalore!/FastQC/MultiQC - Illumina HiSeq Genome Sequencing Data

2018
Geoduck Genome Sequencing
Previous FastQC/MultiQC analysis of the geoduck Illumina HiSeq data (NMP.fastq.gz files) revealed a high level of overrepresented sequences, high levels of Per Base N…
Mar 28, 2018
Sam White
 

FastQC/MultiQC - BGI Geoduck Genome Sequencing Data

2018
Geoduck Genome Sequencing
Since running SparseAssembler seems to be working and actually able to produce assemblies, I’ve decided I’ll try to beef up the geoduck genome assembly with the rest of our…
Mar 27, 2018
Sam White
 

Titrations - Hollie's Seawater Samples

2018
Miscellaneous
All data is deposited in the following GitHub repo:
Mar 27, 2018
Sam White
 

Assembly - Geoduck NovaSeq using SparseAssembler kmer = 101

2018
Geoduck Genome Sequencing
The prior run used a kmer size of 61, and the resulting assembly was rather poor (small N50).
Mar 27, 2018
Sam White
 

Assembly - Geoduck NovaSeq using SparseAssembler (TL;DR - it worked!)

2018
Geoduck Genome Sequencing
The prior attempt using SparseAssembler failed due to a kmer size that was deemed too large.
Mar 22, 2018
Sam White
 

Titrations - Hollie's Seawater Samples

2018
Miscellaneous
All data is deposited in the following GitHub repo:
Mar 20, 2018
Sam White
 

DNA Isolation & Quantification - Geoduck larvae metagenome filter rinses

2018
Miscellaneous
Isolated DNA from two of the geoduck hatchery metagenome samples Emma delivered on 20180313 to get an idea of what type of yields we might get from these.
Mar 20, 2018
Sam White
 

Titrations - Hollie's Seawater Samples

2018
Miscellaneous
Performed total alkalinity (TA) titrations on Hollie’s samples using our T5 Excellence titrator (Mettler Toledo) and Rondolino sample changer.
Mar 19, 2018
Sam White
 

Titrations - Hollie's Seawater Samples

2018
Miscellaneous
Performed total alkalinity (TA) titrations on Hollie’s samples using our T5 Excellence titrator (Mettler Toledo) and Rondolino sample changer.
Mar 16, 2018
Sam White
 

Samples Received - Geoduck larvae metagenome filter rinses

2018
Samples Received
Received geoduck hatchery metagenome samples from Emma. These samples are intended for DNA isolation.
Mar 13, 2018
Sam White
 

Assembly - Geoduck NovaSeq using SparseAssembler (failed)

2018
Geoduck Genome Sequencing
assembly
geoduck
NovaSeq
Panopea generosa
SparseAssembler
Steven came across a 2012 paper in BMC Bioinformatics (“Exploiting sparseness in de novo genome assembly”) that utilized an assembly program we hadn’t previously encountered: …
Mar 8, 2018
Sam White
 

Progress Report - Titrator

2018
CRM
Rondolino
T5
T5 Excellence
titrator
I’ll begin this entry with a TL;DR (becuase it’s definitely a very long read):
Mar 6, 2018
Sam White
 

Ubuntu Installation - Convert Apple Xserve "bigfish" to Ubuntu

2018
Computer Servicing
Due to hardware limitations on the Apple Xserves we have, we can’t use drives >2TB in size. “Bigfish” was set up to be RAID’d and, as such, has three existing HDDs installed.
Feb 28, 2018
Sam White
 

Hardware Upgrades - USB 3.0 PCI Card and 1TB SSD in Woodpecker

2018
Computer Servicing
Installed an additional 1TB SSD and a USB 3.0 PCI card in woodpecker to make it usable for MinION sequencing. An SSD and USB 3.0 ports are just a couple of the hardware…
Feb 28, 2018
Sam White
 

Samples Received - Triploid Crassostrea gigas from Nisbet Oyster Company

2018
Samples Received
Received a bag of Pacific oysters from Nisbet Oyster Company.
Feb 28, 2018
Sam White
 

NovaSeq Assembly - The Struggle is Real - Real Annoying!

2018
Geoduck Genome Sequencing
AllPaths-LG
assembly
geoduck
jr-assembler
meraculous
mox
NovaSeq
Panopea generosa
SOAPdenovo2
Well, I continue to struggle to makek progress on assembling the geoduck Illumina NovaSeq data. Granted, there is a ton of data (374GB!!!!), but it’s still frustrating that…
Feb 21, 2018
Sam White
 

Assembly - Geoduck Illumina NovaSeq SOAPdenovo2 on Mox (FAIL)

2018
Geoduck Genome Sequencing
Trying to get the NovaSeq data assembled using SOAPdenovo2 on the Mox HPC node we have and it will not work.
Feb 19, 2018
Sam White
 

Ethanol Precipitation & DNA Quantification - C. virginica MBD DNA from Yaamini

2018
Samples Submitted
Finished the ethanol precipitation as described in the MethylMiner (Invitrogen) manual which Yaamini had previously initiated: https://yaaminiv.github.io/Virginica-MBDSeq-Day…
Feb 7, 2018
Sam White
 

NovaSeq Assembly - Trimmed Geoduck NovaSeq with Meraculous

2018
Geoduck Genome Sequencing
assembly
geoduck
Illumina
kmer
kmer genie
meraculous
NovaSeq
Panopea generosa
roadrunner
Attempted to use Meraculous to assemble the trimmed geoduck NovaSeq data.
Feb 5, 2018
Sam White
 

Titrator Setup - Functional Methods & Data Exports

2018
Miscellaneous
I’ve been working on getting our T5 Excellence titrator (Mettler Toledo) with Rondolino sample changer (Mettler Toledo) set up and operational.
Feb 1, 2018
Sam White
 

Adapter Trimming and FASTQC - Illumina Geoduck Novaseq Data

2018
Geoduck Genome Sequencing
FASTQC
geoduck
Illumina
multiqc
NovaSeq
Panopea generosa
trim galore
trimming
We would like to get an assembly of the geoduck NovaSeq data that Illumina provided us with.
Jan 25, 2018
Sam White
 

Software Install - 10x Genomics Supernova on Mox (Hyak)

2018
10x genomics
bcl2fastq2
hyak
mox
supernova
Steven asked me to install Supernova (by 10x Genomics on our Mox node.
Jan 22, 2018
Sam White
 

Samples Submitted - C. virginica gDNA, MBD, and MspI to Qiagen

2018
Samples Submitted
Sent Crassostrea virginica samples to Qiagen, as part of the collaboration we have with them for testing their new bisulfite conversion kit on various reduced representation…
Jan 16, 2018
Sam White
 

Assembly Comparisons – Oly Assemblies Using Quast

2018
Olympia Oyster Genome Sequencing
assembly
jupyter notebook
Olympia oyster
Ostrea lurida
QUAST
I ran Quast to compare all of our current Olympia oyster genome assemblies.
Jan 16, 2018
Sam White
 

DNA Quantification - MspI-digested Crassostrea virginica gDNA

2018
Miscellaneous
Quantified the two MspI-digested DNA samples for the Qiagen project from earlier today with the Qubit 3.0 (ThermoFisher).
Jan 11, 2018
Sam White
 

Phenol:Chloroform Extractions and EtOH Precipitations - MspI Digestions of C.virginica DNA from Earlier Today

2018
Crassostrea virginica
Eastern oyster
EtOH precipitation
phenol-chloroform cleanup
The two MspI restriction digestions from earlier today for our project with Qiagen were subjected to phenol:chloroform cleanup and subsequent ethanol precipitations.
Jan 11, 2018
Sam White
 

Restriction Digestion - MspI on Crassotrea virginica gDNA

2018
Miscellaneous
Digested two 1.5μg aliquots of Crassostrea virginica isolated 20171211, as part of the project we’re doing with Qiagen.
Jan 11, 2018
Sam White
 

DNA Quantification - C.virginica MBD-enriched DNA

2018
Crassostrea virginica
DNA Quantification
Eastern oyster
Qubit 3.0
Qubit dsDNA BR
Quantified Crassostrea virginica MBD-enriched DNA from earlier today for Qiagen project.
Jan 10, 2018
Sam White
 

MBD Enrichment – Crassostrea virginica Sheared DNA Day 3

2018
Crassostrea virginica
Eastern oyster
EtOH precipitation
MBD
MBD enrichment
MethylMiner Methylated DNA Enrichment Kit
Continued MBD enrichment of C.virginica DNA from yesterday for Qiagen project.
Jan 10, 2018
Sam White
 

MBD Enrichment – Crassostrea virginica Sheared DNA Day 2

2018
Crassostrea virginica
Eastern oyster
MBD
MBD enrichment
MethylMiner Methylated DNA Enrichment Kit
Continued MBD enrichment for C.virginica and Qiagen project from yesterday.
Jan 9, 2018
Sam White
 

MBD Enrichment - Crassostrea virginica Sheared DNA Day 1

2018
Miscellaneous
As part of a project with Qiagen to have them try out some of our DNA with their newest DNA bisulfite conversion kit, I previously [isolated DNA from Crassotrea virginica (Ea…
Jan 8, 2018
Sam White
 

Tissue Sampling - Crassostrea virginica Tissues for Archiving

2017
Miscellaneous
I figured it’d be prudent to collect some Eastern oyster (Crassotrea virginica) to have around the lab.
Dec 13, 2017
Sam White
 

Software Install - MSMTP For Email Notices of Bash Job Completion on Emu (Ubuntu)

2017
Miscellaneous
After I finally resolved the installation of PB Jelly on Emu (running Ubuntu 16.04), I’ve had a PB Jelly assembly running for the past two weeks! I’ve gotten tired of…
Dec 13, 2017
Sam White
 

Samples Submitted - Pulverized Geoduck Tissues to Illumina for More 10x Genomics Sequencing

2017
Geoduck Genome Sequencing
Samples Submitted
Continuing Illumina’s generous efforts to use our geoduck samples to test out the robustness of their emerging sequencing technologies, they have requested we send them some…
Dec 12, 2017
Sam White
 

DNA Sonication & Bioanalzyer - C. virginica gDNA for MeDIP

2017
Miscellaneous
I transferred 8ug (136uL) of Crassotrea virginica gDNA (isolated earlier today) to two separate 1.7mL snap cap tubes for sonication/shearing.
Dec 11, 2017
Sam White
 

DNA Isolation & Quantification - Crassostrea virginica Mantle gDNA

2017
Miscellaneous
DNA was isolated from a single adult Eastern oyster (Crassostrea virginica) for a pilot project with Qiagen to test their new DNA bisulfite conversion kit. The oyster was…
Dec 11, 2017
Sam White
 

Genome Assembly – Olympia Oyster Illumina & PacBio Using PB Jelly w/BGI Scaffold Assembly

2017
Olympia Oyster Genome Sequencing
After another attempt to fix PB Jelly, I ran it again.
Nov 30, 2017
Sam White
 

Troubleshooting – PB Jelly Install on Emu Continued

2017
Miscellaneous
The last “fix” didn’t fix everything.
Nov 30, 2017
Sam White
 

Samples Submitted - Geoduck Tissues to Illumina for More 10x Genomics Sequencing

2017
Geoduck Genome Sequencing
Samples Submitted
Continuing Illumina’s generous efforts to use our geoduck samples to test out the robustness of their emerging sequencing technologies, they have requested we send them some…
Nov 20, 2017
Sam White
 

Troubleshooting - PB Jelly Install on Emu

2017
Miscellaneous
I previously installed. Despite no error messages being output, I noticed something odd during my quick post-assembly stats check: The PB Jelly numbers were identical to the…
Nov 20, 2017
Sam White
 

DNA Isolation & Quantification - C. virginica Gonad gDNA

2017
Miscellaneous
I isolated DNA from the Crassotrea virginica gonad samples sent by Katie Lotterhos using the E.Z.N.A. Mollusc Kit with the following modifications:
Nov 14, 2017
Sam White
 

Assembly Comparison - Oly Assemblies Using Quast

2017
Olympia Oyster Genome Sequencing
I ran Quast to compare all of our current Olympia oyster genome assemblies.
Nov 14, 2017
Sam White
 

Genome Assembly - Olympia Oyster Illumina & PacBio Using PB Jelly w/BGI Scaffold Assembly

2017
Olympia Oyster Genome Sequencing
Yesterday, I ran PB Jelly using Sean’s Platanus assembly, but that didn’t produce an assembly because PB Jelly was expecting gaps in the Illumina reference assembly…
Nov 14, 2017
Sam White
 

Genome Assembly - Olympia Oyster Illumina & PacBio Using PB Jelly w/Platanus Assembly

2017
Olympia Oyster Genome Sequencing
Sean had previously attempted to run PB Jelly, but ran into some issues running on Hyak, so I decided to try this on Emu.
Nov 13, 2017
Sam White
 

Samples Received - Tanner Crab Hemolymph in RNA Later from Pam Jensen

2017
Samples Received
Tanner Crab RNAseq
Pam Jensen stopped by and dropped off Tanner crab (Chionoecetes bairdi) hemolymph samples (~300) stored in RNA Later (Ambion). Samples were stored at 4C.
Nov 13, 2017
Sam White
 

RNA Isolation & Quantification - Tanner crab hemolymph

2017
Tanner Crab RNAseq
We received three Tanner crab (Chionoecetes bairdi)hemolymph samples from Pam Jensen (NOAA) yesterday. From her email to Steven:
Nov 7, 2017
Sam White
 

Software Installation - ALPACA on Roadrunner

2017
Miscellaneous
List of software that needed installing to run ALPACA:
Oct 31, 2017
Sam White
 

Software Crash - Olympia oyster genome assembly with Masurca on Mox

2017
Miscellaneous
Ah, the joys of bioinformatics. I just received an email from Mox indicating that [the Masurca assembly I started 11 DAYS AGO…
Oct 31, 2017
Sam White
 

Software Installation - PB Jelly Suite and Blasr on Emu

2017
Miscellaneous
I followed along with what Sean previously did when installing on Emu, but it appears he didn’t install it in the shared location to make it accessible to all users. So, I’m…
Oct 30, 2017
Sam White
 

Genome Assembly - Olympia oyster Illumina & PacBio Reads Using Redundans

2017
Olympia Oyster Genome Sequencing
Had problems with Docker and Jupyter Notebook inexplicably dying and deleting all the files in the working directory of the Jupyter Notebook (which also happened to be the…
Oct 24, 2017
Sam White
 

Assembly Comparison - Oly PacBio Canu: Sam vs. Sean with Quast

2017
Miscellaneous
I recently finished an assembly of our Olympia oyster PacBio data using Canu and thought it would be interesting to compare to Sean’s Canu assembly.
Oct 23, 2017
Sam White
 

FAIL - Missing Data on Owl!

2017
Miscellaneous
Uh oh. There appears to be some data that’s been removed from Owl. I noticed this earlier when trying to look at some of Sean’s data. His data should be in a folder with his…
Oct 23, 2017
Sam White
 

Genome Assembly - Olympia oyster Illumina & PacBio reads using MaSuRCA

2017
Olympia Oyster Genome Sequencing
Oct 19, 2017
Sam White
 

Software Installation - MaSuRCA v3.2.3 Assembler on Mox (Hyak)

2017
Miscellaneous
Saw this tweet this morning and thought this would be good to try out for our Olympia oyster genome assemblies, as it will handle “hybrid” assemblies (i.e. short-reads and…
Oct 19, 2017
Sam White
 

Fail - Directory Contents Deleted!

2017
Miscellaneous
Uh, not sure what happened here:
Oct 18, 2017
Sam White
 

Genome Assembly - Olympia oyster PacBio Canu v1.6

2017
Olympia Oyster Genome Sequencing
I decided to run Canu myself, since documentation for Sean’s Canu run is a bit lacking. Additionally, it looks like he specified a genome size of 500Mbp, which is probably…
Oct 18, 2017
Sam White
 

Data Management - Convert Oly PacBio H5 to FASTQ

2017
Olympia Oyster Genome Sequencing
After working with all of this Olympia oyster genome sequencing data, I remembered that we had an old, singular PacBio SMRT cell file (from June 2013). This file didn’t seem…
Oct 9, 2017
Sam White
 

Genome Assembly - Olympia oyster Redundans/Canu vs. Redundans/Racon

2017
Olympia Oyster Genome Sequencing
Decided to compare the Redundans using Canu as reference and Redundans using Racon as reference. Both reference assemblies were just our PacBio data.
Oct 6, 2017
Sam White
 

Genome Assembly - Olympia Oyster Redundans with Illumina + PacBio

2017
Olympia Oyster Genome Sequencing
Redundans should assemble both Illumina and PacBio data, so let’s do that.
Oct 5, 2017
Sam White
 

Genome Assembly - minimap/miniasm/racon Overview

2017
Olympia Oyster Genome Sequencing
Previously, I used the following three tools to do quick assembly of our Olympia oyster PacBio data:
Oct 4, 2017
Sam White
 

Assembly Comparisons - Olympia oyster genome assemblies

2017
Olympia Oyster Genome Sequencing
Having run through this a bunch of times now, I realized that the analysis below incorrectly identifies the outputs from Sean’s Redundans runs. The correct output from each…
Oct 3, 2017
Sam White
 

Samples Received - C.virginica gonad tissue from Katie Lotterhos

2017
Samples Received
Received and stored @-80C in rack 8, row 5, column 5.
Oct 3, 2017
Sam White
 

Goals - October 2017

2017
Goals
I guess one of my primary goals is to make sure I actually write my monthly goals each month.
Oct 2, 2017
Sam White
 

Genome Assembly - Olympia oyster PacBio minimap/miniasm/racon

2017
Miscellaneous
In this GitHub Issue, Steven had suggested I try out the minimap/miniasm/racon pipeline for assembling our Olympia oyster PacBio data.
Sep 18, 2017
Sam White
 

Genome Assembly - Olympia oyster PacBio minimap/miniasm/racon

2017
Olympia Oyster Genome Sequencing
In this GitHub Issue, Steven had suggested I try out the minimap/miniasm/racon pipeline for assembling our Olympia oyster PacBio data.
Sep 18, 2017
Sam White
 

Genome Assembly - Olympia oyster PacBio minimap/miniasm/racon

2017
Olympia Oyster Genome Sequencing
In this GitHub Issue, Steven had suggested I try out the minimap/miniasm/racon pipeline for assembling our Olympia oyster PacBio data.
Sep 7, 2017
Sam White
 

Samples Submitted - Geoduck Ctenidia to Illumina for 10x Genomics Sequencing

2017
Geoduck Genome Sequencing
Samples Submitted
Continuing Illumina’s generous efforts to use our geoduck samples to test out the robustness of their emerging sequencing technologies, they have requested we send them some…
Aug 28, 2017
Sam White
 

Project Progress - Olympia Oyster Genome Assemblies by Sean Bennett

2017
Olympia Oyster Genome Sequencing
Here’s a brief overview of what Sean has done with the Oly genome assembly front.
Aug 28, 2017
Sam White
 

Data Management - Illumina Geoduck HiSeq & MiSeq Data

2017
Geoduck Genome Sequencing
The HDD we received from Illumina last week only had data (i.e. fastq files) from the NovaSeq runs they performed - nothing from either the MiSeq, nor the HiSeq runs.
Aug 8, 2017
Sam White
 

Goals - August 2017

2017
Goals
Data, data, data! That is the theme for this month.
Aug 3, 2017
Sam White
 

Data Received - Geoduck Genome Sequencing by Illumina

2017
Geoduck Genome Sequencing
We previously sent some geoduck samples to Illumina, as part of a pilot project for them to test out a new sequencing platform. The data has finally arrived!
Jul 31, 2017
Sam White
 

Sample Submission - Olympia oyster gonad RNA to Katherine Silliman @ Univ. of Chicago

2017
Samples Submitted
Sent the following RNA to Katherine Silliman at the Univ. of Chicago for RNAseq. All RNA was isolated on 20170719, except SN-10-16, which was isolated on 20170710.
Jul 20, 2017
Sam White
 

RNA Isolation - Olympia oyster gonad tissue in paraffin histology blocks

2017
Miscellaneous
My previous go at this was a little premature - I didn’t wait for Laura to fully annotate her slides/blocks. Little did I know, the tissue was mostly visceral mass and, as…
Jul 19, 2017
Sam White
 

RNA Isolation - Olympia oyster gonad tissue in paraffin histology blocks

2017
Miscellaneous
UPDATE 20170712: The RNA I isolated below is from incorrect regions of tissue. I misunderstood exactly what this tissue was, and admittedly, jumped the gun. The tissue is…
Jul 10, 2017
Sam White
 

Data Management - SRA Submission Olympia Oyster UW PacBio Data from 20170323

2017
Olympia Oyster Genome Sequencing
Submitted the FASTQ files from the UW PacBio Data from 20170323 to the [NCBI sequence read archive (SRA)(https://www.ncbi.nlm.nih.gov/sra).
Jul 6, 2017
Sam White
 

Data Management – Tarball of Olympia oyster UW PacBio Data from 20170323

2017
Olympia Oyster Genome Sequencing
I’d previously attempted to archive this data set on multiple occasions, across multiple days, but network dropouts kept killing my connection to the server (Owl) and, in…
Jul 6, 2017
Sam White
 

Data Management - OLYMPIA OYSTER UW PACBIO DATA (FROM 20170323) TO NIGHTINGALES

2017
Olympia Oyster Genome Sequencing
Added UW PacBio FASTQ files to our nightingales Google Sheet for keeping track of our high-throughput sequencing projects.
Jul 5, 2017
Sam White
 

Sample Annotation - Olympia oyster histology blocks (from Laura Spencer)

2017
Miscellaneous
I’ve been asked to isolate RNA from some paraffin-embedded Olympia oyster gonad tissue.
Jul 5, 2017
Sam White
 

Manuscript Re-submission - Oly Stress Response to PeerJ for Review

2017
Miscellaneous
Last August, we made our initial submission of this paper to PeeJ.
Jul 3, 2017
Sam White
 

Data Management - Olympia oyster UW PacBio Data from 20170323

2017
Olympia Oyster Genome Sequencing
Due to other priorities, getting this PacBio data sorted and prepped for our [next gen sequencing data management plan…
Jul 3, 2017
Sam White
 

GitHub Curation

2017
Miscellaneous
Updated a couple of GitHub Wikis:
Jun 22, 2017
Sam White
 

Goals - June 2017

2017
Goals
Well, my previous goal was to tidy up an existing manuscript and get it re-submitted to PeerJ. That’s pretty much done, as Steven will be giving a final once over and…
Jun 1, 2017
Sam White
 

DNA Methylation Quantification - Acropora cervicornis (Staghorn coral) DNA from Javier Casariego (FIU)

2017
Miscellaneous
Used the MethylFlash Methylated DNA Quantification Kit (Colorimetric) from Epigentek to quantify methylation in these coral DNA samples.
May 11, 2017
Sam White
 

DNA Quantification - Acropora cervicornis (Staghorn coral) DNA from Javier Casariego (FIU)

2017
Miscellaneous
I quantified the three samples (listed below) that I SpeedVac’d yesterday using the the Roberts Lab Qubit 3.0.
May 11, 2017
Sam White
 

DNA Concentration - Acropora cervicornis (Staghorn coral) DNA from Javier Casariego (FIU)

2017
Miscellaneous
Three samples (of the 62 total) that were quantified earlier today, had concentrations too low for use in the methylation assay:
May 10, 2017
Sam White
 

DNA Quantification - Acropora cervicornis (Staghorn coral) DNA from Javier Casariego (FIU)

2017
Miscellaneous
DNA samples received yesterday were quantified using the Roberts Lab Qubit 3.0 to improve quantification accuracy (samples provided by Javier were quantified via NanoDrop…
May 10, 2017
Sam White
 

Samples Received - Olympia oyster Histology Blocks and Slides (for Laura Spencer)

2017
Samples Received
Received histology blocks and slides for Laura Spencer.
May 9, 2017
Sam White
 

Samples Received - Acropora cervicornis (Staghorn coral) DNA from Javier Casariego (FIU)

2017
Samples Received
Received 62 coral (Acropora cervicornis) DNA samples from Javier Casariego at FIU.
May 9, 2017
Sam White
 

Goals - May 2017

2017
Goals
A day late, but definitely not a dollar short!
May 2, 2017
Sam White
 

Manuscript Writing - Submitted!

2017
Genotype-by-sequencing at BGI
(http://eagle.fish.washington.edu/Arabidopsis/20170419_Overleaf_sci_data_oly_gbs_submission.png)
Apr 19, 2017
Sam White
 

Manuscript - Oly GBS 14 Day Plan

2017
Genotype-by-sequencing at BGI
For Pub-a-thon 2017, Steven has asked us to put together a 14 day plan for our manuscripts.
Apr 18, 2017
Sam White
 

Data Received - Olympia oyster PacBio Data

2017
Olympia Oyster Genome Sequencing
Back in December 2016, we sent off Ostrea lurida DNA to the UW PacBio sequencing facility. This is an attempt to fill in the gaps left from the BGI genome sequencing project.
Mar 23, 2017
Sam White
 

Data Management – SRA Submission Oly GBS Batch Submission

2017
Genotype-by-sequencing at BGI
An earlier attempt at submitting these files failed.
Mar 21, 2017
Sam White
 

Computing - Owl Partially Restored

2017
Computer Servicing
Heard back from Synology and they indicated I should click the “Repair” option to fix the System Partition Failed error message seen previously.
Mar 21, 2017
Sam White
 

Data Management - SRA Submission Oly GBS Batch Submission Fail

2017
Genotype-by-sequencing at BGI
[I had previously submitted the two non-demultiplexed genotype-by-sequencing (GBS) files provided by BGI to the NCBI short read archive…
Mar 20, 2017
Sam White
 

Troubleshooting - Synology NAS (Owl) Down After Update

2017
Computer Servicing
TL;DR - Server didn’t recover after firmware update last night. “Repair” is an option listed in the web interface, but I want to confirm with Synology what will happen…
Mar 18, 2017
Sam White
 

Computing – Oly BGI GBS Reproducibility; fail?

2017
Genotype-by-sequencing at BGI
OK, so things have improved since the last attempt at getting this BGI script to run and demultiplex the raw data.
Mar 17, 2017
Sam White
 

Computing – Oly BGI GBS Reproducibility Fail (but, less so than last time)...

2017
BS-seq Libraries for Sequencing at Genewiz
Well, my previous attempt at reproducing the demultiplexing that BGI performed was an exercise in futility. BGI got back to me with the following message:
Mar 14, 2017
Sam White
 

Computing - Oly BGI GBS Reproducibility Fail

2017
Genotype-by-sequencing at BGI
Since we’re preparing a manuscript that relies on BGI’s manipulation/handling of the genotype-by-sequencing data, I attempted to could reproduce the demultiplexing steps…
Mar 7, 2017
Sam White
 

FASTQC - Oly BGI GBS Raw Illumina Data Demultiplexed

2017
Genotype-by-sequencing at BGI
Last week, I ran the two raw FASTQ files through FastQC. As expected, FastQC detected “errors”. These errors are due to the presence of adapter sequences, barcodes, and the…
Mar 7, 2017
Sam White
 

FASTQC - Oly BGI GBS Raw Illumina Data

2017
Genotype-by-sequencing at BGI
Below, is the Jupyter notebook I used to run the FastQC analysis on the two files. I’ve embedded for quick viewing, but it might be easier to view the notebook via the…
Mar 2, 2017
Sam White
 

Goals - March 2017

2017
Goals
Oh, actually, there is another, smaller goal that will be very difficult to achieve: win Pub-a-Thon. Jay’s taken a massive lead and has a nearly complete manuscript ready…
Mar 1, 2017
Sam White
 

Manuscript Writing - More "Nuances" Using Authorea

2017
Miscellaneous
I previously highlighted some of the issues I was having using Authorea.com as an writing platform.
Feb 28, 2017
Sam White
 

Data Received - Jay's Coral RADseq and Hollie's Geoduck Epi-RADseq

2017
Miscellaneous
Jay received notice from UC Berkeley that the sequencing data from his coral RADseq was ready. In addition, the sequencing contains some epiRADseq data from samples provided…
Feb 27, 2017
Sam White
 

Data Management - SRA Submission of Ostrea lurida GBS FASTQ Files

2017
Genotype-by-sequencing at BGI
SRA Submissions
Prepared a short read archive (SRA) submission for archiving our Olympia oyster genotype-by-sequencing (GBS) data in NCBI. This is in preparation for submission of the mansuc…
Feb 8, 2017
Sam White
 

Goals - February 2017

2017
Goals
First goal is to be the first person in lab to post their goals each month. Props to one of our new grad students, Yaamini Venkataraman on beating me this month!
Feb 2, 2017
Sam White
 

Manuscript Writing - The "Nuances" of Using Authorea

2017
Genotype-by-sequencing at BGI
Miscellaneous
PROBLEM: Authorea spits out a browser-crashing “unresponsive script” message (actually, lots and lots of them; clicking “Stop script” or “Continue” just results in…
Jan 23, 2017
Sam White
 

Sample Submission – Geoduck gDNA for Illumina Pilot Sequencing Project

2017
Geoduck Genome Sequencing
Samples Submitted
Sent 10μg of the geoduck gDNA I isolated earlier today to Illumina on dry ice via FedEx Standard Overnight service.
Jan 5, 2017
Sam White
 

DNA Isolation - Geoduck gDNA for Illumina-initiated Sequencing Project

2017
Geoduck Genome Sequencing
We were previously approached by Cindy Lawley (Illumina Market Development) for possible participation in an Illumina product development project, in which they wanted to…
Jan 5, 2017
Sam White
 

Data Management - Replacement of Corrupt BGI Oly Genome FASTQ Files

2017
Olympia Oyster Genome Sequencing
Previously, Sean and Steven identified two potentially corrupt FASTQ files. I contacted BGI about getting replacement files and they informed me that all versions of the…
Jan 4, 2017
Sam White
 

Goals - January 2017

2017
Goals
One of the long-running goals I’ve had is to get this Oly GBS data taken care of and out the door to publication. I think I will finally succeed with this, with the help of P…
Jan 3, 2017
Sam White
 

Data Management - Geoduck RRBS Data Integrity Verification

2016
geoduck
jupyter notebook
md5
Panopea generosa
RRBS
Yesterday, I downloaded the Illumina FASTQ files provided by Genewiz for Hollie Putnam’s reduced representation bisulfite geoduck libraries. However, Genewiz had not…
Dec 30, 2016
Sam White
 

Data Received - Geoduck RRBS Sequencing Data

2016
Genewiz
geoduck
Illumina
Panopea generosa
RRBS
Hollie Putnam prepared some reduced representation bisulfite Illumina libraries and had them sequenced by Genewiz.
Dec 29, 2016
Sam White
 

Sample Submission - Geoduck Tissue & gDNA for Illumina Pilot Sequencing Project

2016
Geoduck Genome Sequencing
Samples Submitted
geoduck
Illumina
Panopea generosa
Sent the following samples to Illumina for possible selection in a new pilot sequencing platform they’re working on.
Dec 21, 2016
Sam White
 

DNA Isolation - Geoduck gDNA for Potential Illumina-initiated Sequencing Project

2016
Geoduck Genome Sequencing
DNA Isolation
E.Z.N.A. Mollusc Kit
gel
geoduck
O'geneRuler DNA Ladder Mix
Panopea generosa
Qubit 3.0
Qubit dsDNA BR
We were approached by Cindy Lawley (Illumina Market Development) yesterday to see if we’d be able to participate in some product development. We agreed and need some geoduck…
Dec 21, 2016
Sam White
 

Sample Submission - Geoduck Reduced Representation Bisulfite Pooled Libraries

2016
Samples Submitted
geoduck
Hollie Putnam
Panopea generosa
RRBS
Hollie Putnam asked me to help her get samples ready for submission for Illumina sequencing at Genewiz.
Dec 20, 2016
Sam White
 

Sample Submission - Ostrea lurida gDNA for PacBio Sequencing

2016
Olympia Oyster Genome Sequencing
Samples Submitted
gDNA
olympia oyster
Ostrea lurida
PacBio
Submitted 10μg (30.7μL) of the O.lurida gDNA I isolated on 20161214 to the UW PacBio facility - Order #450.
Dec 19, 2016
Sam White
 

Data Management - Integrity Check of Final BGI Olympia Oyster & Geoduck Data

2016
Geoduck Genome Sequencing
Olympia Oyster Genome Sequencing
After completing the downloads of these files from BGI, I needed to verify that the downloaded copies matched the originals. Below is a Jupyter Notebook detailing how I…
Dec 15, 2016
Sam White
 

DNA Isolation - Ostrea lurida DNA for PacBio Sequencing

2016
Olympia Oyster Genome Sequencing
DNA Isolation
DNA Quantification
E.Z.N.A. Mollusc Kit
gDNA
gel
olympia oyster
Ostrea lurida
Qubit 3.0
Qubit dsDNA BR
In an attempt to improve upon the partial genome assembly we received from BGI, we will be sending DNA to the UW PacBio core facility for additional sequencing.
Dec 14, 2016
Sam White
 

Data Management - Trim Output Cells from Jupyter Notebook

2016
jupyter notebook
Last week I downloaded the final BGI data files and assemblies for Olympia oyster and geoduck genome sequencing projects. However, the output from the download command made…
Dec 14, 2016
Sam White
 

Data Management - Download Final BGI Genome & Assembly Files

2016
Geoduck Genome Sequencing
Olympia Oyster Genome Sequencing
BGI
geoduck
jupyter notebook
olympia oyster
Ostrea lurida
owl
Panopea generosa
We received info to download the final data and genome assembly files for geoduck and Olympia oyster from BGI.
Dec 14, 2016
Sam White
 

Goals - December 2016

2016
Goals
Well, I’ve finally progressed with the Olly GBS analysis!
Dec 1, 2016
Sam White
 

Data Analysis - Continued O.lurida Fst Analysis from GBS Data

2016
Genotype-by-sequencing at BGI
Olympia oyster reciprocal transplant
Continued the analysis I started the other day. Still following Katherine Silliman’s notebook for guidance.
Dec 1, 2016
Sam White
 

Computing - An Excercise in Futility

2016
jupyter notebook
R
Trying to continue my Oly GBS analsyis from the other day and follow along with Katherine Silliman’s notebook
Nov 30, 2016
Sam White
 

Data Analysis - Initial O.lurida Fst Determination from GBS Data

2016
Genotype-by-sequencing at BGI
Olympia oyster reciprocal transplant
docker
dockerfile
FST
jupyter notebook
olympia oyster
Ostrea lurida
vcftools
Finally running some analysis on the output from my PyRad analysison 20160727.
Nov 17, 2016
Sam White
 

Data Management - Tracking O.lurida FASTQ File Corruption

2016
Olympia Oyster Genome Sequencing
UPDATE 20170104 - These two corrupt files have been replaced with non-corrupt files.
Nov 17, 2016
Sam White
 

Computer Management - Additional Configurations for Reformatted Xserves

2016
Computer Servicing
Sean got the remaining Xserves configured to run independently from the master node of the cluster they belonged to and installed OS X 10.11 (El Capitan).
Nov 16, 2016
Sam White
 

Data Management - Modify Eagle/Owl Cloud Sync Account

2016
Computer Servicing
Re-examining our backup options for our two Synology servers (Eagle & Owl), I realized that they were both backing up to the just my account on UW’s unlimited Google Drive…
Nov 7, 2016
Sam White
 

Computing - Retrieve data from Amazon EC2 Instance

2016
Genotype-by-sequencing at BGI
Olympia oyster reciprocal transplant
I had an existing instance that still had data on it from my PyRad analysis on 20160727 that I needed to retrieve.
Nov 4, 2016
Sam White
 

Goals - November 2016

2016
Goals
Well, I’m serious this time. My goal for this month is to complete the Oly GBS data analysis and, get the data sets and data analysis prepared/placed in satisfactory…
Nov 2, 2016
Sam White
 

Data Management – Geoduck Small Insert Library Genome Assembly from BGI

2016
Geoduck Genome Sequencing
BGI
geoduck
jupyter notebook
Panopea generosa
Received another set of Panopea generosa genome assembly data from BGI back in May! I neglected to create MD5 checksums, as well as a readme file for this data set! Of…
Oct 25, 2016
Sam White
 

Goals - October 2016

2016
Goals
Last month’s goals, as it turns out, were way too ambitious. This month’s goal will be to get the Oly GBS data analysis fully completed (currently have individuals data, but…
Oct 3, 2016
Sam White
 

Data Received – Jay’s Coral epiRADseq - Not Demultiplexed

2016
Miscellaneous
Previously downloaded Jay’s epiRADseq data that was provided by the Genomic Sequencing Laboratory at UC-Berkeley. It was provided already demultiplexed (which is very nice…
Sep 19, 2016
Sam White
 

Oyster Sampling - Olympia Oyster OA Populations at Manchester

2016
Miscellaneous
I helped Katherine Silliman with her oyster sampling today from her ocean acidification experiment with Olympia oysters (Ostrea lurida) at the Kenneth K. Chew Center for…
Sep 12, 2016
Sam White
 

Data Received - Jay's Coral epiRADseq

2016
coral
epiRAD
Porites
RAD
RAD-seq
We received notice that Jay’s coral (Porites spp) epiRADseq ( dead onsnetwork link jdimond/2016/08/02/rad-sequencing-days-12/) data was available from the Genomic Sequencing…
Sep 8, 2016
Sam White
 

Goals - September 2016

2016
Goals
Whoops! It’s already September 6th! The 1st of the month came and went without me noticing.
Sep 6, 2016
Sam White
 

Data Management - Synology Cloud Sync to UW Google Drive

2016
Computer Servicing
After a bit of a scare this weekend (Synology DX513 expansion unit no longer detected two drives after a system update - resolved by powering down the system and rebooting…
Aug 29, 2016
Sam White
 

Server HDD Failure – Owl

2016
Computer Servicing
Noticed that Owl (Synology DS1812+ server) was beeping.
Aug 22, 2016
Sam White
 

Manuscript Submission - Oly Stress Response to PeerJ for Review

2016
Miscellaneous
Submitted the following manuscript to PeerJ for peer review:
Aug 18, 2016
Sam White
 

Data Analysis - fastStructure Population Analysis of Oly GBS PyRAD Output

2016
Genotype-by-sequencing at BGI
fastStructure
jupyter notebook
olympia oyster
Ostrea lurida
Structure
After some basal readings about what Fst is (see notebook below for a definition and reference), I decided to try to use fastStructure to analyze the PyRAD output from 201607…
Aug 16, 2016
Sam White
 

Computing - Amazon EC2 Cost "Analysis"

2016
computing
EC2
Xserve
I recently moved some computing jobs over to Amazon’s Elastic Cloud Computing (EC2) in attempt to avoid some odd computing issues/errors I kept encountering on our lab…
Aug 1, 2016
Sam White
 

Goals - August 2016

2016
Goals
Complete Olympia oyster GBS data analysis - Progress has actually been made! After many struggles, I managed to get a PyRad analysis of the entire data set to complete. Now…
Aug 1, 2016
Sam White
 

Data Analysis - PyRad Analysis of Olympia Oyster GBS Data

2016
Genotype-by-sequencing at BGI
docker
EC2
jupyter notebook
olympia oyster
Ostrea lurida
pyrad
Previously, I ran a PyRad analysis on just a subset of these samples in an attempt to have some data for a grant pre-proposal.
Jul 27, 2016
Sam White
 

Computing - Not Enough Power!

2016
computing
EC2
jupyter notebook
pyrad
stacks
ustacks
Well, I tackled the storage space issue by expanding the EC2 Instance to have a 1000GB of storage space. Now that that’s no longer a concern, it turns out I’m running up…
Jul 18, 2016
Sam White
 

Computing - Amazon EC2 Instance Out of Space?

2016
Genotype-by-sequencing at BGI
Olympia oyster reciprocal transplant
Running PyRad analysis on the Olympia oyster GBS data. PyRad exited with warnings about running out of space. However, looking at free disk space on the EC2 Instance…
Jul 17, 2016
Sam White
 

Computing - A Very Quick "Guide" to Amazon EC2 Continued

2016
Miscellaneous
Yesterday’s post ended with me trying to mount a S3 bucket to my EC2 instance using s3fs-fuse.
Jul 14, 2016
Sam White
 

Dissection - Frozen Geoduck & Pacific Oyster

2016
Miscellaneous
We’re working on a project with Washington Department of Natural Resources’ (DNR) Micah Horwith to identify potential proteomic biomarkers in geoduck (Panopea generosa) and …
Jul 14, 2016
Sam White
 

Filter Replacement - Xserve Server Rack Enclosure

2016
Computer Servicing
Replaced the filters on the rack enclosure that houses the Apple Xserver server blades we have in the lab.
Jul 14, 2016
Sam White
 

Computing - The Very Quick "Guide" to Amazon Web Services Cloud Computing Instances (EC2)

2016
Miscellaneous
This all takes a surprisingly long time to set up.
Jul 13, 2016
Sam White
 

DNA Methylation Quantification - Coral DNA from Jose M. Eirin-Lopez (Florida International University)

2016
Miscellaneous
Ran the coral DNA I quantified on 20160630 through the MethylFlash Methylated DNA Quantification Kit [Colorimetric] (Epigentek) kit to quantify global methylation.
Jul 7, 2016
Sam White
 

Goals - July 2016

2016
Goals
Unfortunately, most of this month’s goals are the same as last months!
Jul 1, 2016
Sam White
 

DNA Quantification - Coral DNA from Jose M. Eirin-Lopez (Florida International University)

2016
Miscellaneous
Quantified the DNA we received from Jose on 20160615 using the Qubit 3.0 Flouorometer (ThermoFisher) with the dsDNA Broad Range (BR) Kit according to the manufacturer’s…
Jun 30, 2016
Sam White
 

Samples Received - Coral DNA from Jose M. Eirin-Lopez (Florida International University)

2016
Samples Received
Steven received these coral DNA samples today. Here’s his post on Google Plus (stored @ 4C in FTR 213):
Jun 15, 2016
Sam White
 

Docker - VirtualBox Defaults on OS X

2016
Computer Servicing
I noticed a discrepancy between what system info is detected natively on Roadrunner (Apple Xserve) and what was being shown when I started a Docker container.
Jun 14, 2016
Sam White
 

Docker - One liner to create Docker container

2016
Miscellaneous
One liner to create Docker container for Jupyter notebook usage and data analysis on roadrunner (Xserve):
Jun 9, 2016
Sam White
 

RAM Upgrade - Roadrunner (Apple Xserve) to 48GB RAM

2016
Computer Servicing
We received the new 48GB RAM set we ordered from Other World Computing for the Apple Xserve (roadrunner) that I installed El Capitan (OS X 10.11.5) on two weeks ago.
Jun 9, 2016
Sam White
 

Goals - June 2016

2016
Goals
Current goals are as follows:
Jun 6, 2016
Sam White
 

Docker - Improving Roberts Lab Reproducibility

2016
Computer Servicing
In an attempt at furthering our lab’s abilities to maximize our reproducibility, I’ve been  working on developing an all-encompassing Docker image. Docker is a type of…
Jun 1, 2016
Sam White
 

Computer Setup - Cluster Node003 Conversion

2016
Computer Servicing
Here’s an overview of some of the struggles getting node003 converted/upgraded to function as an independent computer (as opposed to a slave node in the Apple computer…
May 31, 2016
Sam White
 

Data Analysis - Oly GBS Data Using Stacks 1.37

2016
Genotype-by-sequencing at BGI
BGI
GBS
genotype-by-sequencing
ipython notebook
jupyter notebook
olympia oyster
Ostrea lurida
stacks
This analysis ran (or, more properly, was attempted) for a couple of weeks and failed a few times. The failures seemed to be linked to the external hard drive I was…
May 23, 2016
Sam White
 

Data Management - Olympia Oyster Small Insert Library Genome Assembly from BGI

2016
Olympia Oyster Genome Sequencing
BGI
ipython notebook
jupyter notebook
olympia oyster
Ostrea lurida
Received another set of Ostrea lurida genome assembly data from BGI. In this case, it’s data assembled from the small insert libraries they created for this project.
May 16, 2016
Sam White
 

GBS Frustrations

2016
Miscellaneous
This isn’t really a notebook entry - it’s more of a traditional blog post.
May 3, 2016
Sam White
 

Goals - May 2016

2016
Goals
Well, I guess the first goal is to remember to be more consistent about writing monthly goals…
May 2, 2016
Sam White
 

SRA Release - Transcriptomic Profiles of Adult Female & Male Gonads in Panopea generosa (Pacific geoduck)

2016
Protein expression profiles during sexual maturation in Geoduck
SRA Submissions
geoduck
Panopea generosa
PRJNA316216
SRA
SRP072283
SRX1659865
SRX1659866
The RNAseq data that I previously submitted to NCBI short read archive (SRA) has been released to the public today. Here are the various links for the project:
Apr 28, 2016
Sam White
 

Data Management - O.lurida Raw BGI GBS FASTQ Data

2016
Genotype-by-sequencing at BGI
Olympia oyster reciprocal transplant
BGI had previously supplied us with demultiplexed GBS FASTQ files. However, they had not provided us with the information/data on how those files were created. I contacted…
Apr 27, 2016
Sam White
 

Computing - Speed Benchmark Comparisons Between Local, External, & Server Files

2016
Miscellaneous
I decided to run a quick test to see what difference in speed (i.e. time) we might see between handling files that are stored locally, on an external hard drive (HDD), or on…
Apr 27, 2016
Sam White
 

Data Analysis - Subset Olympia Oyster GBS Data from BGI as Single Population Using PyRAD

2016
Genotype-by-sequencing at BGI
Attempting to get some sort of analysis of the Ostrea lurida GBS data from BGI, particularly since the last run at it using Stacks crashed (literally) and burned (not…
Apr 18, 2016
Sam White
 

Data Management - Concatenate FASTQ files from Oly MBDseq Project

2016
MBD Enrichment for Sequencing at ZymoResearch
Olympia oyster reciprocal transplant
Steven requested I concatenate the MBDseq files we received for this project:
Apr 11, 2016
Sam White
 

Data Analysis - Oly GBS Data from BGI Using Stacks

2016
Genotype-by-sequencing at BGI
UPDATE (20160418) : I’m posting this more for posterity, as Stacks continually locked up at both the “ustacks” and “cstacks” stages. These processes would take days to run…
Apr 6, 2016
Sam White
 

Software Install - samtools-0.1.19 and stacks-1.37

2016
Computer Servicing
Getting ready to analyze our Ostrea lurida genotype-by-sequencing data and wanted to use the Stacks software.
Apr 6, 2016
Sam White
 

SRA Submission – Genome sequencing of the Olympia oyster (Ostrea lurida)

2016
Olympia Oyster Genome Sequencing
SRA Submissions
NCBI
olympia oyster
Ostrea lurida
PRJNA316624
SAMN04588827
SRA
SRP072461
SRS1365663
SRX1667397
SRX1667398
SRX1667399
SRX1667400
SRX1667401
SRX1667402
Adding our Olympia oyster genome sequencing (sequencing done by BGI) to the NCBI Sequence Read Archive (SRS). The current status can be seen in the screen cap below. Release…
Mar 28, 2016
Sam White
 

SRA Submission – Genome sequencing of the Pacific geoduck (Panopea generosa)

2016
Geoduck Genome Sequencing
SRA Submissions
geoduck
NCBI
Panopea generosa
SRA
PRJNA316601
Adding our geoduck genome sequencing (sequencing done by BGI) to the NCBI Sequence Read Archive (SRS). The current status can be seen in the screen cap below. Release date…
Mar 28, 2016
Sam White
 

SRA Submission - Transcriptomic Profiles of Adult Female & Male Gonads in Panopea generosa (Pacific geoduck).

2016
Protein expression profiles during sexual maturation in Geoduck
geoduck
NCBI
Panopea generosa
SRA
SRP072283
RNAseq experiment, which is part of a larger project that involves characterizing geoduck gonad development across multiple stages: histologically, proteomically, and…
Mar 24, 2016
Sam White
 

SRA Submission - Individual Transcriptomic Profiles of C.gigas Before & After Heat Shock

2016
SRA Submissions
RNA-seq experiment conducted by Claire in 2013.
Mar 23, 2016
Sam White
 

Data Management - SRA Submission Overview

2016
Miscellaneous
We have an enormous backlog of high-throughput sequencing files (641 FASTQ files, to be exact) that we need/want to get added to the NCBI Sequence Read Archive (SRA).
Mar 23, 2016
Sam White
 

Data Management - O. lurida genotype-by-sequencing (GBS) data from BGI

2016
Genotype-by-sequencing at BGI
We received a hard drive from BGI on 20160223 (while I was out on paternity leave) containing the Ostrea lurida GBS data.
Mar 14, 2016
Sam White
 

Data Received - Initial Geoduck Genome Assembly from BGI

2016
Geoduck Genome Sequencing
The initial assembly of the Ostrea lurida genome is available from BGI. Currently, we’ve stashed it here:
Mar 14, 2016
Sam White
 

Data Received - Initial Olympia oyster Genome Assembly from BGI

2016
Olympia Oyster Genome Sequencing
The initial assembly of the Ostrea lurida genome is available from BGI. Currently, we’ve stashed it here:
Mar 14, 2016
Sam White
 

Data Management - O.lurida 2bRAD Dec2015 Undetermined FASTQ files

2016
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
2bRAD
ipython notebook
jupyter notebook
olympia oyster
Ostrea lurida
RAD
RAD-seq
An astute observation by Katherine Sillimanrevealed that the FASTQ files I had moved to our high-throughput sequencing archive on our server Owl, only had two FASTQ files…
Mar 8, 2016
Sam White
 

Data Management - High-throughput Sequencing Data

2016
fusion table
nightingales
owl
We’ve had a recent influx of sequencing data, which is great, but it created a bit of a backlog documenting what we’ve received.
Feb 4, 2016
Sam White
 

Data Received - Ostrea lurida MBD-enriched BS-seq

2016
MBD Enrichment for Sequencing at ZymoResearch
Olympia oyster reciprocal transplant
Received the Olympia oyster, MBD-enriched BS-seq sequencing files (50bp, single read) from ZymoResearch (submitted 20151208). Here’s the sample list:
Feb 3, 2016
Sam White
 

Data Received - Ostrea lurida genome sequencing files from BGI

2016
Olympia Oyster Genome Sequencing
Downloaded data from the BGI project portal to our server, Owl, using the Synology Download Station. Although the BGI portal is aesthetically nice, it’s set up poorly for…
Jan 27, 2016
Sam White
 

Data Received - Panopea generosa genome sequencing files from BGI

2016
Geoduck Genome Sequencing
Downloaded data from the BGI project portal to our server, Owl, using the Synology Download Station. Although the BGI portal is aesthetically nice, it’s set up poorly for…
Jan 27, 2016
Sam White
 

Data Analysis - Identification of duplicate files on Eagle

2016
Computer Servicing
Recently, we’ve been bumping into our storage limit on Eagle (our Synology DS413):
Jan 14, 2016
Sam White
 

Data Received - Bisulfite-treated Illumina Sequencing from Genewiz

2016
BS-seq Libraries for Sequencing at Genewiz
Olympia oyster reciprocal transplant
Received notice the sequencing data was ready from Genewiz for the samples submitted 20151222.
Jan 8, 2016
Sam White
 

Data Received - Oly 2bRAD Illumina Sequencing from Genewiz

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
The data was made available to use on 20151224 and took two days to download.
Dec 31, 2015
Sam White
 

Sample Submission - BS-seq Library Pool to Genewiz

2015
BS-seq Libraries for Sequencing at Genewiz
Olympia oyster reciprocal transplant
Samples Submitted
Pooled 10ng of each of the libraries prepared yesterday with [TruSeq DNA Methylation Library Kit…
Dec 22, 2015
Sam White
 

Illumina Methylation Library Quantification - BS-seq Oly/C.gigas Libraries

2015
BS-seq Libraries for Sequencing at Genewiz
Olympia oyster reciprocal transplant
Re-quantified the libraries that were completed yesterday using the Qubit3.0 dsDNA HS (high sensitivity) assay because the library concentrations were too low for the normal…
Dec 22, 2015
Sam White
 

Illumina Methylation Library Construction - Oly/C.gigas Bisulfite-treated DNA

2015
BS-seq Libraries for Sequencing at Genewiz
Olympia oyster reciprocal transplant
Took the bisulfite-treated DNA from 20151218 and made Illumina libraries using the [TruSeq DNA Methylation Library Kit…
Dec 21, 2015
Sam White
 

Bioanalyzer - Bisulfite-treated Oly/C.gigas DNA

2015
BS-seq Libraries for Sequencing at Genewiz
Olympia oyster reciprocal transplant
Following the guidelines of the [TruSeq DNA Methylation Library Prep Guide…
Dec 18, 2015
Sam White
 

Reagent Prep - RNA Pico 6000 Ladder

2015
Reagent Prep
Prepared the RNA Pico 6000 ladder (Agilent) according to the manufacturer’s protocol:
Dec 18, 2015
Sam White
 

Bisulfite Treatment - Oly Reciprocal Transplant DNA & C.gigas Lotterhos DNA for BS-seq

2015
BS-seq Libraries for Sequencing at Genewiz
Olympia oyster reciprocal transplant
After confirming that the DNA available for this project looked good, I performed bisulfite treatment on the following gDNA samples:
Dec 18, 2015
Sam White
 

Agarose Gel - Oly gDNA for BS-seq Libraries, Take Two

2015
BS-seq Libraries for Sequencing at Genewiz
Olympia oyster reciprocal transplant
The gel I ran earlier today looked real rough, due to the fact that I didn’t bother to equalize loading quantities of samples (I just loaded 1μL of all samples regardless of…
Dec 17, 2015
Sam White
 

Agarose Gel - Oly gDNA for BS-seq Libraries

2015
BS-seq Libraries for Sequencing at Genewiz
Olympia oyster reciprocal transplant
Ran 1μL of each sample from yesterday’s DNA isolation on a 0.8% agarose, low-TAE gel, stained with ethidium bromide.
Dec 17, 2015
Sam White
 

DNA Isolation - Oly gDNA for BS-seq

2015
BS-seq Libraries for Sequencing at Genewiz
Olympia oyster reciprocal transplant
1NF11
1NF12
1NF13
1NF14
1NF15
1NF16
1NF17
1NF18
2NF1
2NF2
2NF3
2NF4
2NF5
2NF6
2NF7
2NF8
BS-seq
chloroform
DNA Isolation
DNA Quantification
DNazol
Fidalgo Bay
olympia oyster
Ostrea lurida
Oyster Bay
Qubit 3.0
Qubit dsDNA BR
RNAse A
Need DNA to prep our own libraries for bisulfite-treated high-throughput sequencing (BS-seq).
Dec 16, 2015
Sam White
 

Sample Submission - 2bRAD Libraries for Genewiz

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
Samples Submitted
Pooled the libraries into a single sample for sequencing on Illumina HiSeq2500 by Genewiz.
Dec 10, 2015
Sam White
 

Samples Received - C.gigas Tissue & DNA from Katie Lotterhos

2015
Samples Received
Received 6 samples from Katie today. The box was labeled and stored @ -20C.
Dec 10, 2015
Sam White
 

Sample Submission - Olympia oyster MBD-enriched DNA to ZymoResearch

2015
MBD Enrichment for Sequencing at ZymoResearch
Olympia oyster reciprocal transplant
Samples Submitted
We opted to go with ZymoResearch for this project because they could do the bisulfite treatment and finish the sequencing by the end of January.
Dec 8, 2015
Sam White
 

Sample Submission - Additional Olympia Oyster gDNA for Genome Sequencing @ BGI

2015
Olympia Oyster Genome Sequencing
Samples Submitted
Yep, BGI still needs more gDNA for the Olympia oyster genome sequencing project. Samples have been quantified via dye-based fluorescence, as opposed to the NanoDrop, so our…
Dec 1, 2015
Sam White
 

Sample Submission - Additional Geoduck gDNA for Genome Sequencing @ BGI

2015
Geoduck Genome Sequencing
Yep, BGI still needs more gDNA for the geoduck genome sequencing project. Samples have been quantified via dye-based fluorescence, as opposed to the NanoDrop, so our…
Dec 1, 2015
Sam White
 

Data Storage - Synology DX513

2015
Computer Servicing
Running a bit low on storage on Owl (Synology DS1812+) and we will be receiving a ton of data in the next few months, so we purchased a Synology DX513. It’s an expansion…
Nov 30, 2015
Sam White
 

Sample Submission - Oly Oyster Bay Tissues for GBS

2015
Genotype-by-sequencing at BGI
Olympia oyster reciprocal transplant
Samples Submitted
Sent Olympia oyster tissue samples to BGI for genotype-by-sequencing (GBS). Tissues were shipped FedEx standard overnight on dry ice.
Nov 30, 2015
Sam White
 

Samples Received - Oly Tissue & DNA from Katherine Silliman

2015
Olympia oyster reciprocal transplant
Samples Received
Samples were stored @ -20C in FTR 209.
Nov 25, 2015
Sam White
 

DNA Quality Assessment - Geoduck & Olympia Oyster gDNA

2015
Geoduck Genome Sequencing
Olympia Oyster Genome Sequencing
gDNA
gel
geoduck
O'geneRuler DNA Ladder Mix
olympia oyster
Ostrea lurida
Panopea generosa
Have three separate sets of geoduck & olympia oyster gDNA that need to be run on gels before sending to BGI for genome sequencing:
Nov 25, 2015
Sam White
 

DNA Isolation - Olympia Oyster Outer Mantle gDNA

2015
Olympia Oyster Genome Sequencing
chloroform
DNA Isolation
DNA Quantification
DNazol
gDNA
mantle
NanoDrop1000
olympia oyster
Ostrea lurida
Qubit 3.0
Qubit dsDNA BR
Isolated additional gDNA for the genome sequencing. To try to improve the quality (260/280 & 260/230 ratios) of the gDNA, I added a chloroform step after the initial tissue…
Nov 25, 2015
Sam White
 

DNA Isolation - Geoduck Ctenidia gDNA

2015
Geoduck Genome Sequencing
chloroform
ctenidia
DNA Isolation
DNA Quantification
DNazol
gDNA
geoduck
NanoDrop1000
Panopea generosa
Qubit 3.0
Qubit dsDNA BR
Isolated additional gDNA for the genome sequencing. In an attempt to obtain better yields, I used ctenidia (instead of adductor muscle). Additionally, to try to improve the…
Nov 25, 2015
Sam White
 

Phenol-Chloroform DNA Cleanup - Geoduck gDNA

2015
Geoduck Genome Sequencing
DNA Quantification
gDNA
geoduck
NanoDrop1000
Panopea generosa
phenol-chloroform cleanup
Quant-iT DNA BR Kit
Victor 1420 plate reader
The gDNA I extracted on 20151104 didn’t look great on the NanoDrop so I decided to perform a phenol-chloroform cleanup to see if I could improve the NanoDrop1000 absorbance…
Nov 24, 2015
Sam White
 

Phenol-Chloroform DNA Cleanup - Olympia Oyster gDNA

2015
Olympia Oyster Genome Sequencing
The gDNA I extracted on 20151104 didn’t look great on the NanoDrop so I decided to perform a phenol-chloroform cleanup to see if I could improve the NanoDrop1000 absorbance…
Nov 24, 2015
Sam White
 

DNA Isolation - Geoduck Adductor Muscle gDNA

2015
Geoduck Genome Sequencing
DNA Isolation
DNA Quantification
gDNA
geoduck
NanoDrop1000
Panopea generosa
Quant-iT DNA BR Kit
Victor 1420 plate reader
Since we still don’t have sufficient gDNA for the full scope of the genome sequencing, I isolated more gDNA.
Nov 24, 2015
Sam White
 

DNA Isolation - Olympia Oyster Outer Mantle gDNA

2015
Olympia Oyster Genome Sequencing
DNA Isolation
DNA Quantification
E.Z.N.A. Mollusc Kit
gDNA
NanoDrop1000
olympia oyster
Ostrea lurida
Quant-iT DNA BR Kit
Victor 1420 plate reader
Since we still don’t have sufficient gDNA for the full scope of the Olympia oyster genome sequencing, I isolated more gDNA.
Nov 24, 2015
Sam White
 

DNA Quantification - MBD-enriched Olympia oyster DNA

2015
MBD Enrichment for Sequencing at ZymoResearch
Olympia oyster reciprocal transplant
DNA Quantification
MBD
MBD-Seq
olympia oyster
Ostrea lurida
plate reader
Quant-iT DNA BR Kit
Victor 1420 plate reader
Quantified the MBD enriched samples prepped over the last two days: MBD enrichment, EtOH precipiation.
Nov 23, 2015
Sam White
 

Ethanol Precipitation - Olympia oyster MBD

2015
MBD Enrichment for Sequencing at ZymoResearch
Olympia oyster reciprocal transplant
EtOH precipitation
MethylMiner Methylated DNA Enrichment Kit
olympia oyster
Ostrea lurida
Precipitated the MBD enriched DNA from yesterday according to the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) protocol.
Nov 22, 2015
Sam White
 

MBD Enrichment - Sonicated Olympia Oyster gDNA

2015
MBD Enrichment for Sequencing at ZymoResearch
Olympia oyster reciprocal transplant
hc1_2B
hc1_4B
hc2_15B
hc2_17
hc3_1
hc3_10
hc3_11
hc3_5
hc3_7
hc3_9
Hood Canal
MethylMiner Methylated DNA Enrichment Kit
olympia oyster
Ostrea lurida
Oyster Bay
ss2_14B
ss2_18B
ss2_9B
ss3_14B
ss3_15B
ss3_16B
ss3_20
ss3_3B
ss3_4B
ss5_18
Olympia oyster gDNA that had previously been sonicated and fragmented was enriched for the methylated fragments using the MethylMiner Methylated DNA Enrichment Kit…
Nov 21, 2015
Sam White
 

DNA Sonication - Oly gDNA for MBD

2015
MBD Enrichment for Sequencing at ZymoResearch
bioanalyzer
Bioruptor 300
electropherogram
hc1_2B
hc1_4B
hc2_15B
hc2_17
hc3_1
hc3_10
hc3_11
hc3_5
hc3_7
hc3_9
Hood Canal
olympia oyster
Ostrea lurida
Oyster Bay
sonication
ss2_14B
ss2_18B
ss2_9B
ss3_14B
ss3_15B
ss3_16B
ss3_20
ss3_3B
ss3_4B
ss5_18
In preparation for MBD enrichment, fragmented Olympia oyster gDNA with a target size of ~350bp.
Nov 19, 2015
Sam White
 

qPCR – Oly RAD-Seq Library Quantification

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
2bRAD
KAPA Library Illumina Quantification Kit
olympia oyster
Opticon
Opticon2
Ostrea lurida
qPCR
RAD
RAD-seq
After yesterday’s attempt at quantification revealed insufficient dilution of the libraries, I repeated the qPCRs using 1:100000 dilutions of each of the libraries. Used the…
Nov 17, 2015
Sam White
 

qPCR - Oly RAD-Seq Library Quantification

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
2bRAD
KAPA Library Illumina Quantification Kit
olympia oyster
Opticon
Opticon2
Ostrea lurida
qPCR
RAD
RAD-seq
The final step before sequencing these 2bRAD libraries is to quantify them. Used the KAPA Illumina Quantification Kit (KAPA Biosystems) according to the manufacturer’s…
Nov 16, 2015
Sam White
 

Gel Extraction - Oly RAD-Seq Prep Scale PCR

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
2bRAD
gel extraction
olympia oyster
Ostrea lurida
QIAQuick Gel Extraction Kit
RAD
RAD-seq
Extracted the PCR products from the gel slices from 20151114 using the QIAQuick Gel Extraction Kit (Qiagen) according to the manufacturer’s protocol. Substituted MiniElute…
Nov 16, 2015
Sam White
 

DNA Quality Assessment - Geoduck, Oly & Oly 2SN

2015
Geoduck Genome Sequencing
Olympia Oyster Genome Sequencing
Olympia oyster reciprocal transplant
Fidalgo 2SN
gDNA
gel
geoduck
O'geneRuler DNA Ladder Mix
olympia oyster
Ostrea lurida
Panopea generosa
I recently ran gDNA isolated for geoduck and Olympia oyster genome sequencing, as well as gDNA isolated from the Olympia oyster reciprocal transplant experiment out on a…
Nov 13, 2015
Sam White
 

PCR – Oly RAD-seq Prep Scale PCR

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
barcodes
gel
ILL-BC1
ILL-BC10
ILL-BC2
ILL-BC3
ILL-BC4
ILL-BC5
ILL-BC6
ILL-BC7
ILL-BC8
ILL-BC9
ILL-HT1
olympia oyster
Ostrea lurida
PCR
PTC-200
Q5 High-Fidelity DNA Polymerase
RAD
RAD-seq
Continuing with the RAD-seq library prep. Following the Meyer Lab 2bRAD protocol. After determining the minimum number of PCR cycles to run to generate a visible, 166bp band…
Nov 13, 2015
Sam White
 

PCR – Oly RAD-seq Test-scale PCR

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
gel
ILL-BC1
ILL-HT1
ILL-LIB1
ILL-LIB2
O'geneRuler DNA Ladder Mix
olympia oyster
Ostrea lurida
PCR
PTC-200
RAD
RAD-seq
Continuing with the RAD-seq library prep. Following the Meyer Lab 2bRAD protocol.
Nov 12, 2015
Sam White
 

DNA Quantification & Quality Assessment - Oly 2SN gDNA

2015
Olympia oyster reciprocal transplant
bioanalyzer
DNA Quantification
Fidalgo 2SN
gDNA
NanoDrop1000
olympia oyster
Ostrea lurida
Comparison of three different approaches to using the E.Z.N.A. Mollusc Kit:
Nov 4, 2015
Sam White
 

DNA Quantification & Quality Assessment - Geoduck & Oly gDNA

2015
Geoduck Genome Sequencing
Olympia Oyster Genome Sequencing
bioanalyzer
DNA Quantification
gDNA
geoduck
NanoDrop1000
olympia oyster
Ostrea lurida
Panopea generosa
Quantified the following samples with the Roberts Lab NanoDrop1000 (ThermoFisher) and assessed DNA integrity on the Seeb Lab Bioanalyzer 2100 (Agilent) using the DNA 12000…
Nov 4, 2015
Sam White
 

DNA Isolations – Oly Fidalgo 2SN Ctenidia

2015
Olympia oyster reciprocal transplant
DNA Isolation
E.Z.N.A. Mollusc Kit
Fidalgo 2SN
gDNA
olympia oyster
Ostrea lurida
Isolated DNA from 24 2SN ctenidia samples from Friday’s sampling (#32 - 55). Samples were thawed at RT.
Nov 3, 2015
Sam White
 

Oyster Sampling - Oly Fidalgo 2SN, 2HL, 2NF Reciprocal Transplants Final Samplings

2015
Olympia oyster reciprocal transplant
ctenidia
E.Z.N.A. Mollusc Kit
Fidalgo 2HL
Fidalgo 2NF
Fidalgo 2SN
gill
olympia oyster
Ostrea lurida
RNAlater
The remaining Olympia oysters from Jake Heare’s reciprocal transplant experiment have been retrieved from field sites and are awaiting sampling. The oysters have been stored…
Oct 30, 2015
Sam White
 

DNA Isolation – Geoduck & Olympia Oyster

2015
Geoduck Genome Sequencing
Olympia Oyster Genome Sequencing
DNA Isolation
DNA Quantification
gDNA
geoduck
NanoDrop1000
olympia oyster
Ostrea lurida
Panopea generosa
Amazingly, we need more gDNA for the two genome sequencing projects (geoduck and Olympia oyster). Used geoduck adductor muscle sample from Box 1 of the geoduck samples…
Oct 29, 2015
Sam White
 

Adaptor Ligation – Oly AlfI-Digested gDNA for RAD-seq

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
3ILL-NR
5ILL-NR
anti-ILL
gDNA
ligation
olympia oyster
Ostrea lurida
PTC-200
RAD-seq
T4 DNA Ligase
Continued to follow the 2bRAD protocol (PDF) developed by Eli Meyer’s lab.
Oct 29, 2015
Sam White
 

Restriction Digest – Oly gDNA for RAD-seq w/AlfI

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
2bRAD
AlfI
gDNA
olympia oyster
Ostrea lurida
RAD-seq
restriction digestion
The previous attempt at making these RAD libraries failed during the prep-scale PCR, likely due to a discrepancy in the version of the Meyer Lab protocol I was following, so…
Oct 28, 2015
Sam White
 

Troubleshooting - Oly RAD-seq

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
RAD
RAD-seq
troubleshooting
Oddly, it turns out that Katherine’s version of the Meyer Lab 2bRAD protocol differed from what I had download. To add to the confusion, both protocols have the same file…
Oct 23, 2015
Sam White
 

DNA Isolations - Fidalgo 2SN Reciprocal Transplants Final Samplings

2015
Olympia oyster reciprocal transplant
ctenidia
DNA Isolation
E.Z.N.A. Mollusc Kit
Fidalgo 2SN
olympia oyster
Ostrea lurida
RNAlater
The remaining Olympia oysters from Jake Heare’s reciprocal transplant experiment have been retrieved from field sites and are awaiting sampling. The oysters have been stored…
Oct 21, 2015
Sam White
 

PCR - Oly RAD-seq Prep Scale PCR

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
gel
ILL-BC1
ILL-BC10
ILL-BC2
ILL-BC3
ILL-BC4
ILL-BC5
ILL-BC6
ILL-BC7
ILL-BC8
ILL-BC9
ILL-HT1
ILL-LIB1
ILL-LIB2
olympia oyster
Ostrea lurida
PCR
PTC-200
Q5 High-Fidelity DNA Polymerase
RAD-seq
Continuing with the RAD-seq library prep. Following the Meyer Lab 2bRAD protocol.
Oct 13, 2015
Sam White
 

PCR - Oly RAD-seq Test-scale PCR

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
gel
ILL-BC1
ILL-HT1
ILL-LIB1
ILL-LIB2
O'geneRuler DNA Ladder Mix
olympia oyster
Ostrea lurida
PCR
PTC-200
RAD
RAD-seq
Continuing with the RAD-seq library prep. Following the Meyer Lab 2bRAD protocol.
Oct 12, 2015
Sam White
 

Adaptor Ligation – Oly AlfI-Digested gDNA for RAD-seq

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
3ILL-NR
5ILL-NR
anti-ILL
ligation
olympia oyster
Ostrea lurida
PTC-200
RAD-seq
T4 DNA Ligase
Continued to follow the 2bRAD protocol (PDF) developed by Eli Meyer’s lab.
Oct 9, 2015
Sam White
 

Restriction Digest – Oly gDNA for RAD-seq w/AlfI

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
Used a subset (10 samples) from the Ostrea lurida gDNA isolated 20150917 to prepare RAD libraries.
Oct 9, 2015
Sam White
 

Sample Submission - Additional Geoduck gDNA for Genome Sequencing @ BGI

2015
Geoduck Genome Sequencing
'1510071003'
gDNA
geoduck
Panopea generosa
Samples Submitted
Previous shipment of gDNA proved to be of insufficient quantity when assessed by BGI, so needed to isolate more.
Oct 6, 2015
Sam White
 

Sample Submission - Additional Olympia Oyster gDNA for Genome Sequencing @ BGI

2015
Olympia Oyster Genome Sequencing
Samples Submitted
'1510071002'
gDNA
olympia oyster
Ostrea lurida
Previous shipment of gDNA proved to be of insufficient quantity when assessed by BGI, so needed to isolate more.
Oct 6, 2015
Sam White
 

Agarose Gel - Geoduck & Olympia Oyster gDNA

2015
Geoduck Genome Sequencing
Olympia Oyster Genome Sequencing
Olympia oyster reciprocal transplant
gDNA
gel
geoduck
NF1A
olympia oyster
Ostrea lurida
Panopea generosa
SN49A
Needed to assess the integrity of the newest gDNA isolated for the two genome sequencing projects: Geoduck gDNA from earlier today and Olympia oyster gDNA from 20151003.
Oct 5, 2015
Sam White
 

DNA Quantification - Pooled geoduck gDNA

2015
Geoduck Genome Sequencing
DNA Quantification
gDNA
geoduck
NanoDrop1000
Panopea generosa
Pooled the gDNA samples from earlier today & from 20151003.
Oct 5, 2015
Sam White
 

gDNA Isolation - Geoduck Adductor Muscle

2015
adductor muscle
DNA Isolation
DNA Quantification
DNazol
gDNA
geoduck
NanoDrop1000
Panopea generosa
My isolation on Friday didn’t yield a sufficient quantity of gDNA for the additional DNA needed for the geoduck genome sequencing project. Used two adductor muscles (Box 1)…
Oct 5, 2015
Sam White
 

DNA Isolation - Geoduck & Olympia Oyster

2015
Geoduck Genome Sequencing
Olympia Oyster Genome Sequencing
Olympia oyster reciprocal transplant
adductor muscle
DNA Isolation
DNA Quantification
DNazol
foot
geoduck
NanoDrop1000
NF1A
olympia oyster
Ostrea lurida
Panopea generosa
RNAse A
SN49A
Amazingly, we need more gDNA for the two genome sequencing projects (geoduck and Olympia oyster). Used geoduck “foot 1” sample from Box 1 of the foot samples collected by…
Oct 2, 2015
Sam White
 

PCR - Oly RAD-seq Test-scale PCR

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
gel
ILL-BC1
ILL-HT1
ILL-LIB1
ILL-LIB2
O'geneRuler DNA Ladder Mix
olympia oyster
Ostrea lurida
PCR
PTC-200
Q5 High-Fidelity DNA Polymerase
RAD-seq
Yesterday’s test scale PCR failed to produce any bands in any samples (expected size of ~166bp). This is not particularly surprising, due to the level of degradation in…
Oct 2, 2015
Sam White
 

PCR - Oly RAD-seq Test-scale PCR

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
Reagent Prep
gel
ILL-BC1
ILL-HT1
ILL-HT2
ILL-LIB1
ILL-LIB2
O'geneRuler DNA Ladder Mix
olympia oyster
Ostrea lurida
PCR
PTC-200
Q5 High-Fidelity DNA Polymerase
RAD-seq
Continuing with the RAD-seq library prep. Following the Meyer Lab 2bRAD protocol.
Oct 1, 2015
Sam White
 

Adaptor Ligation - Oly AlfI-Digested gDNA for RAD-seq

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
Reagent Prep
3ILL-NR
5ILL-NR
anti-ILL
ILL-BC1
ILL-HT1
ILL-HT2
ILL-LIB1
ILL-LIB2
ligation
olympia oyster
Ostrea lurida
PTC-200
RAD-seq
T4 DNA Ligase
Yesterday’s AlfI over night restriction digest was heat inactivated by heating @ 65C for 10mins. Samples were stored on ice.
Oct 1, 2015
Sam White
 

Goals - October 2015

2015
Goals
geoduck
olympia oyster
Ostrea lurida
Panopea generosa
I’d review last month’s goals, but I completely forgot to post them!
Oct 1, 2015
Sam White
 

Restriction Digest - Oly gDNA for RAD-seq w/AlfI

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
Reagent Prep
AlfI
gDNA
olympia oyster
Ostrea lurida
RAD-seq
restriction digestion
Used a subset (10 samples) from the Ostrea lurida gDNA isolated 20150916 to prepare RAD libraries. This will be done to assess whether or not these samples, which appear to…
Sep 30, 2015
Sam White
 

Sample Submission - Olympia Oyster gDNA for Genome Sequencing @ BGI

2015
Olympia Oyster Genome Sequencing
Samples Submitted
1509191001
gDNA
olympia oyster
Ostrea lurida
Shipped the pooled gDNA we’ve been accumulating to BGI to initiate the Olympia oyster genome sequencing project.
Sep 21, 2015
Sam White
 

Sample Submission - Geoduck gDNA for Genome Sequencing @ BGI

2015
Geoduck Genome Sequencing
1509191002
gDNA
geoduck
Panopea generosa
Samples Submitted
Shipped the pooled gDNA we’ve been accumulating to BGI to initiate the geoduck genome sequencing project.
Sep 21, 2015
Sam White
 

Uninterruptible Power Supplies (UPS)

2015
Computer Servicing
Eagle
Opticon
owl
Synology
uninterruptible power supply
UPS
A new UPS we installed this week for our qPCR machine (Opticon2 - BioRad) to handle power surges and power outages doesn’t seem to be working properly. With the qPCR machine…
Sep 18, 2015
Sam White
 

Agarose Gel - Geoduck & Olympia oyster gDNA Integrity Check

2015
Geoduck Genome Sequencing
Olympia Oyster Genome Sequencing
gDNA
gel
geoduck
O'geneRuler DNA Ladder Mix
olympia oyster
Ostrea lurida
Panopea generosa
Ran a 0.8% agarose, 1x modified TAE gel (w/EtBr) with geoduck and Olympia oyster gDNA that was precipitated earlier today. Used 5μL of each sample (~500ng).
Sep 17, 2015
Sam White
 

Ethanol Precipitation - Geoduck & Olympia oyster gDNA

2015
Geoduck Genome Sequencing
Olympia Oyster Genome Sequencing
DNA Quantification
EtOH precipitation
geoduck
NanoDrop1000
olympia oyster
Ostrea lurida
Panopea generosa
Pooled all of the geoduck gDNA from all the previous geoduck isolations for the Geoduck Genome Sequencing Project and pooled all of the Ostrea lurida gDNA from previous…
Sep 17, 2015
Sam White
 

Agarose Gel - Olympia oyster Whole Body gDNA Integrity Check

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
gDNA
gel
O'geneRuler DNA Ladder Mix
olympia oyster
Ostrea lurida
Ran the gDNA isolated yesterday from Ostrea lurida whole body on a 0.8% modified TAE gel (w/EtBr) to assess gDNA integrity. Used 1μL of each sample.
Sep 17, 2015
Sam White
 

DNA Isolation - Olympia oyster whole body

2015
2bRAD Library Tests for Sequencing at Genewiz
Olympia oyster reciprocal transplant
DNA Isolation
DNA Quantification
E.Z.N.A. Mollusc Kit
gDNA
NanoDrop1000
olympia oyster
Ostrea lurida
Continued the extractions that Steven began yesterday (dead link - onsnetwork.org/halfshell/2015/09/15/upon-improving-extractions/) and this morning (dead link -…
Sep 16, 2015
Sam White
 

Agarose Gel – Geoduck gDNA Integrity Check

2015
Geoduck Genome Sequencing
gDNA
gel
geoduck
O'geneRuler DNA Ladder Mix
Panopea generosa
Ran 0.8% agarose 1x modified TAE gel stained with EtBr to assess the integrity of geoduck gDNA isolated earlier today.
Sep 16, 2015
Sam White
 

Genomic DNA Isolation – Geoduck Adductor Muscle & Foot

2015
Geoduck Genome Sequencing
DNA Isolation
DNA Quantification
DNazol
gDNA
geoduck
NanoDrop1000
Panopea generosa
Just need a tad bit more gDNA for the geoduck genome sequencing project with BGI. Currently have ~69 and need a minimum of 73μg.
Sep 16, 2015
Sam White
 

Agarose Gel - Geoduck & Olympia Oyster gDNA Integrity Check

2015
Geoduck Genome Sequencing
Olympia Oyster Genome Sequencing
gDNA
gel
geoduck
O'geneRuler DNA Ladder Mix
olympia oyster
Ostrea lurida
Panopea generosa
Ran 0.8% agarose 1x modified TAE gel stained with EtBr to assess the integrity of geoduck gDNA and Olympia oyster gDNA isolated earlier today.
Sep 15, 2015
Sam White
 

Genomic DNA Isolation – Olympia oyster adductor musle & mantle

2015
Olympia Oyster Genome Sequencing
DNA Isolation
DNA Quantification
DNazol
gDNA
NanoDrop1000
olympia oyster
Ostrea lurida
Isolated gDNA from Ostrea lurida (Olympia oyster) adductor muscle & mantle samples collected by Brent & Steven on 20150812 using DNAzol (Molecular Research Center) according…
Sep 15, 2015
Sam White
 

Genomic DNA Isolation – Geoduck Adductor Muscle & Foot

2015
Geoduck Genome Sequencing
DNA Isolation
DNA Quantification
DNazol
gDNA
geoduck
NanoDrop1000
Panopea generosa
Isolated gDNA from Panopea generosa (geoduck) adductor muscle & foot samples collected by Brent & Steven on 20150811 using the DNAzol (Molecular Research Center) according…
Sep 15, 2015
Sam White
 

Agarose Gel - Geoduck & Olympia Oyster gDNA Integrity Check

2015
Geoduck Genome Sequencing
Olympia Oyster Genome Sequencing
gDNA
gel
geoduck
O'geneRuler DNA Ladder Mix
olympia oyster
Ostrea lurida
Panopea generosa
Ran 0.8% agarose 1x modified TAE gel stained with EtBr to assess the integrity of geoduck gDNA and Olympia oyster gDNA isolated yesterday.
Sep 15, 2015
Sam White
 

Genomic DNA Isolation - Olympia oyster adductor musle & mantle

2015
Olympia Oyster Genome Sequencing
adductor muscle
DNA Isolation
DNA Quantification
gDNA
mantle
NanoDrop1000
olympia oyster
Ostrea lurida
Previously isolated gDNA from these tissues on 20150902. However, found out after the isolations that BGI needs >73μg of gDNA for the genome sequencing project, which is…
Sep 14, 2015
Sam White
 

Genomic DNA Isolation - Geoduck Adductor Muscle & Foot

2015
Geoduck Genome Sequencing
adductor muscle
DNA Isolation
DNA Quantification
DNazol
foot
gDNA
geoduck
NanoDrop1000
Panopea generosa
Previously isolated gDNA from these tissues on 20150829. However, found out after the isolations that BGI needs >73μg of gDNA for the genome sequencing project, which is…
Sep 14, 2015
Sam White
 

Agarose Gel - Geoduck & Olympia Oyster gDNA Integrity Check

2015
Geoduck Genome Sequencing
Olympia Oyster Genome Sequencing
gDNA
gel
geoduck
O'geneRuler DNA Ladder Mix
olympia oyster
Ostrea lurida
Panopea generosa
Ran 0.8% agarose 1x modified TAE gel stained with EtBr to assess the integrity of geoduck gDNA (from 20150829) and Olympia oyster gDNA (from 20150902).
Sep 1, 2015
Sam White
 

Genomic DNA Isolation - Olympia oyster adductor musle & mantle

2015
Olympia Oyster Genome Sequencing
DNA Isolation
DNA Quantification
E.Z.N.A. Mollusc Kit
gDNA
NanoDrop1000
olympia oyster
Ostrea lurida
Isolated gDNA from Ostrea lurida (Olympia oyster) adductor muscle & mantle samples collected by Brent & Steven on 20150812 using the E.Z.N.A Mollusc DNA Kit (Omega Bio-Tek)…
Sep 1, 2015
Sam White
 

Server Email Notifications Fix - Eagle

2015
Computer Servicing
Eagle
server
Synology
The system was previously set to use Steven’s Comcast SMTP server. Sending a test email from Eagle failed, indicating authentication failure. I changed this to use the…
Sep 1, 2015
Sam White
 

Genomic DNA Isolation - Geoduck Adductor Muscle & Foot

2015
Geoduck Genome Sequencing
adductor muscle
DNA Isolation
DNA Quantification
E.Z.N.A. Mollusc Kit
foot
gDNA
geoduck
NanoDrop1000
Panopea generosa
Isolated gDNA from Panopea generosa (geoduck) adductor muscle & foot samples collected by Brent & Steven on 20150811 using the E.Z.N.A Mollusc DNA Kit (Omega Bio-Tek)…
Aug 28, 2015
Sam White
 

RAD-Seq Library Prep Reagents

2015
2bRAD Library Tests for Sequencing at Genewiz
Reagent Prep
AlfI
RAD-seq
A box with the above title was established in the -20C in FTR 209 containing the following:
Aug 19, 2015
Sam White
 

SsoFast EvaGreen Supermix Aliquots

2015
Reagent Prep
SsoFast EvaGreen Supermix
Prepared sterile, ~1.5mL aliquots of SsoFast EvaGreen Supermix (received 20150810) in 2.0mL screw cap tubes. All aliquots were dated and stored @ -20C in the “PCR Supplies”…
Aug 11, 2015
Sam White
 

Reverse Transcription – O.lurida DNased RNA 1hr post-mechanical stress

2015
Olympia oyster reciprocal transplant
cDNA
ctenidia
DNased RNA
gill
mechanical stress
olympia oyster
Ostrea lurida
reverse transcriptase
reverse transcription
Performed reverse transcription on the Olympia oyster DNased RNA from the 1hr post-mechanical stress samples from Jake’s project. To accommodate the large numbers of…
Aug 6, 2015
Sam White
 

qPCR - Jake's O.lurida ctenidia 1hr post-mechanical stress DNased RNA

2015
Olympia oyster reciprocal transplant
actin
ctenidia
DNased RNA
gill
mechanical stress
olympia oyster
Opticon2
Ostrea lurida
qPCR
'SR ID: 1504'
'SR ID: 1505'
SsoFast EvaGreen Supermix
Ran qPCR on DNased RNA from earlier today to assess whether there was any residual gDNA after the DNase treatment with Oly_Actin_F/R primers (SR IDs: 1505, 1504).
Aug 6, 2015
Sam White
 

RNA Quantification - O.lurida 1hr post-mechanical heat stress DNased RNA

2015
Olympia oyster reciprocal transplant
ctenidia
DNased RNA
gill
mechanical stress
NanoDrop1000
olympia oyster
Ostrea lurida
RNA quantification
DNased RNA from 20150727 was quantified using the Roberts Lab NanoDrop1000.
Aug 6, 2015
Sam White
 

Goals - August 2015

2015
Goals
RNA has been isolated and DNased from Jake’s mechanically stressed samples.
Aug 3, 2015
Sam White
 

Sample Submission – Olympia oyster PCRs Sanger Sequencing

2015
Olympia oyster reciprocal transplant
Samples Submitted
Submitted a plate of purified PCR products (PCR products prepared by Jake on 20150625) that Jake set up 20150625, to the UW High-Throughput Genomics Center for Sanger…
Jul 31, 2015
Sam White
 

Server HDD Failure - Owl

2015
Computer Servicing
hard drive
HDD
owl
server
Synology
We had our first true test of the Synology RAID redundancy with our Synology 1812+ server (Owl). One of the hard drives (HDD) failed. All of the other drives were fine, the…
Jul 31, 2015
Sam White
 

DNase Treatment - O.lurida Ctenidia 1hr Post-Mechanical Stress RNA

2015
Olympia oyster reciprocal transplant
ctenidia
DNase
gill
NanoDrop1000
olympia oyster
Ostrea lurida
RNA
RNA quantification
Turbo DNA-free
Quantified the RNA I isolated from Jake’s samples on 20150716 using the Roberts Lab NanoDrop1000 (ThermoFisher).
Jul 27, 2015
Sam White
 

RNA Isolation – O.lurida Ctenidia 1hr Post-Mechanical Stress

2015
Olympia oyster reciprocal transplant
ctenidia
gill
mechanical stress
olympia oyster
Ostrea lurida
RNA isolation
RNAzol RT
Isolated RNA from Jake’s Ostrea lurida ctenidia samples that had been subjected to mechanical stress (from 20150422).
Jul 15, 2015
Sam White
 

RNA Isolation - O.lurida Ctenidia 1hr Post-Mechanical Stress

2015
Olympia oyster reciprocal transplant
ctenidia
gill
mechanical stress
olympia oyster
Ostrea lurida
RNA
RNA isolation
RNAzol RT
Isolated RNA from Jake’s Ostrea lurida ctenidia samples that had been subjected to mechanical stress (from 20150422).
Jul 10, 2015
Sam White
 

SsoFast EvaGreen Supermix Aliquots

2015
Reagent Prep
Prepared sterile, 1.0mL aliquots of SsoFast EvaGreen Supermix (received today) in 2.0mL screw cap tubes. All aliquots were dated and stored @ -20C in the “PCR Supplies” box.
Jul 10, 2015
Sam White
 

Automatic Notebook Backups - wget Script & Synology Task Scheduler

2015
Computer Servicing
backup
script
Synology
wget
I’ve been tweaking a shell script (notebook_backups.sh) to use the shell program wget to retrieve fully functional HTML versions of our online notebooks for offline viewing.…
Jul 2, 2015
Sam White
 

PCR - Sea Pen luciferase

2015
Apex Red Master Mix
gDNA
gel
luciferase
O'GeneRuler 100bp DNA ladder
PCR
Renilla reniformis
sea pen
Ran a PCR to obtain luciferase DNA for sequencing.
Jul 2, 2015
Sam White
 

GOALS - July 2015

2015
Goals
Before we check out this month’s goals, let’s have a quick review of last month’s goals and which, if any, I was able to accomplish:
Jul 2, 2015
Sam White
 

Opticon2 Calibration

2015
calibration
FAM
Opticon
Opticon2
qPCR
troubleshooting
Jake and Steven recently noticed localized “hot spots” on most of Jake’s recent qPCRs, where higher levels of fluorescence were consistently showing up in interior portions…
Jun 30, 2015
Sam White
 

RNAseq Data Receipt - Geoduck Gonad RNA 100bp PE Illumina

2015
Protein expression profiles during sexual maturation in Geoduck
geoduck
Geo_pool_F
Geo_pool_M
gonad
Illumina
Panopea generosa
RNA-seq
Data Received
Received notification that the samples sent on 20150601 for RNAseq were completed.
Jun 30, 2015
Sam White
 

Sample Submission – Olympia oyster PCRs Sanger Sequencing

2015
HTGC
olympia oyster
Ostrea lurida
PCR
Sanger sequencing
Samples Submitted
Submitted a plate of purified PCR products (PCR products prepared by Jake on 20150623) that Jake set up yesterday, to the UW High-Throughput Genomics Centerfor Sanger…
Jun 25, 2015
Sam White
 

Reverse Transcription - O.lurida DNased RNA Controls and 1hr Heat Shock

2015
DNased RNA
M-MLV
oligo dT
olympia oyster
Ostrea lurida
reverse transcription
Performed reverse transcription on the Olympia oyster DNased RNA from the control samples and the 1hr heat shock samples of Jake’s project. To accommodate the large numbers…
Jun 17, 2015
Sam White
 

Sample Submission – Olympia oyster & Sea Pen PCRs Sanger Sequencing

2015
olympia oyster
Ostrea lurida
Renilla reniformis
Sanger sequencing
sea pen
Sample Submitted
Prepared two DNA plates and corresponding primer plates for sequencing at the UW HTGC from the purified gel-purified PCRs from yesterday. Primer plates were prepared by…
Jun 16, 2015
Sam White
 

Gel Purification - Olympia Oyster and Sea Pen PCRs

2015
DNA
gel purification
olympia oyster
Ostrea lurida
PCR
Renilla reniformis
sea pen
Ultrafree-DA
Purified DNA from the remaining PCR bands excised by Jake on 20150609 and 20150610, as well as Jonathan’s sea pen PCRs from 20150604 (previously avaiable in…
Jun 15, 2015
Sam White
 

Sample Submission - Olympia oyster PCRs Sanger Sequencing

2015
HTGC
olympia oyster
Ostrea lurida
PCR
Sanger sequencing
Samples Submitted
Submitted a plate of purified PCR products (PCR products prepared by Jake on 20150609 and 20150610) that Jake set up yesterday, to the UW High-Throughput Genomics Center for…
Jun 12, 2015
Sam White
 

Sample Submission - Geoduck Gonad for RNA-seq

2015
Protein expression profiles during sexual maturation in Geoduck
DNased RNA
geoduck
Geo_pool_F
Geo_pool_M
gonad
HiSeq2500
Illumina
Panopea generosa
RNA-seq
Samples Submitted
Prepared two pools of geoduck RNA for RNA-seq (Illumina HiSeq2500, 100bp, PE) with GENEWIZ, Inc.
Jun 1, 2015
Sam White
 

Goals - June 2015

2015
Goals
Before we check out this month’s goals, let’s have a quick review of last month’s goals and which, if any, I was able to accomplish.
Jun 1, 2015
Sam White
 

Bioanalyzer - Geoduck Gonad RNA Quality Assessment

2015
Protein expression profiles during sexual maturation in Geoduck
bioanalyzer
DNased RNA
electropherogram
gel
geoduck
gonad
NanoDrop1000
Panopea generosa
Before proceeding with transcriptomics for this project, we need to assess the integrity of the RNA via Bioanalyzer.
May 27, 2015
Sam White
 

Reverse Transcription - Subset of Jake's O.lurida DNased RNA

2015
cDNA
ctenidia
DNased RNA
gill
heat shock
M-MLV
oligo dT
olympia oyster
Ostrea lurida
reverse transcriptase
reverse transcription
Currently don’t have sufficient reagents to perform reverse transcription on the entire set of DNased RNA (control O.lurida ctenidia samples). To enable Jake to start…
May 22, 2015
Sam White
 

Bioinformatics – Trimmomatic/FASTQC on C.gigas Larvae OA NGS Data

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
bioinformatics
BS-seq
Crassostrea gigas
FASTQC
Illumina
ipython notebook
jupyter notebook
NGS sequencing
Pacific oyster
Trimmomatic
Previously trimmed the first 39 bases of sequence from reads from the BS-Seq data in an attempt to improve our ability to map the reads back to the C.gigas genome. However…
May 22, 2015
Sam White
 

qPCR - Re-run Jake's O.lurida DNased RNA Samples NC1, SC1, SC2, SC4 from 20150514

2015
actin
DNased RNA
olympia oyster
Opticon
Opticon2
Ostrea lurida
qPCR
'SR ID: 1504'
'SR ID: 1505'
SsoFast EvaGreen Supermix
The following DNased RNA samples showed inconsistencies between qPCR reps (one rep showed amplification, the other rep did not) on 20150515:
May 21, 2015
Sam White
 

qPCR – Jake's O.lurida ctenidia DNased RNA (1hr Heat Shock Samples)

2015
actin
ctenidia
DNased RNA
gill
olympia oyster
Opticon
Opticon2
Ostrea lurida
qPCR
'SR ID: 1504'
'SR ID: 1505'
SsoFast EvaGreen Supermix
Ran qPCR on DNased RNA from earlier today to assess whether there was any residual gDNA after the DNase treatment with Oly_Actin_F/R primers (SR IDs: 1505, 1504).
May 14, 2015
Sam White
 

qPCR – Jake's O.lurida ctenidia DNased RNA (Control Samples)

2015
actin
ctenidia
DNased RNA
gill
olympia oyster
Ostrea lurida
qPCR
'SR ID: 1504'
'SR ID: 1505'
SsoFast EvaGreen Supermix
Ran qPCR on DNased RNA from earlier today to assess whether there was any residual gDNA after the DNase treatment with Oly_Actin_F/R primers (SR IDs: 1505, 1504).
May 14, 2015
Sam White
 

DNase Treatment - Jake's O.lurida Ctenidia RNA (1hr Heat Shock) from 20150506

2015
DNase
DNased RNA
NanoDrop1000
olympia oyster
Ostrea lurida
RNA
RNA quantification
Turbo DNA-free
Since the O.lurida RNA I isolated on 20150507 showed residual gDNA via qPCR, I treated 1.5μg of RNA from each sample using the Turbo DNA-free Kit (Ambion/Life Technologies)…
May 14, 2015
Sam White
 

DNase Treatment - Jake's O.lurida Ctenidia RNA (Controls) from 20150507

2015
DNase
DNased RNA
NanoDrop1000
olympia oyster
Ostrea lurida
RNA
RNA quantification
Turbo DNA-free
Since the O.lurida RNA I isolated on 20150507 showed residual gDNA via qPCR, I treated 5μg of RNA from each sample using the Turbo DNA-free Kit (Ambion/Life Technologies)…
May 14, 2015
Sam White
 

ISO Creation - OpticonMonitor3 Disc Cloning

2015
Computer Servicing
Apple
disk image
ISO
Opticon
OS X
software
Since many newer computers are coming without optical disc drives (including my laptop, which I want to install this software on), I created an .iso disc image of the…
May 14, 2015
Sam White
 

qPCR - Jake O.lurida ctenidia RNA (Heat Shock Samples) from 20150506

2015
actin
ctenidia
gill
heat shock
olympia oyster
Opticon2
Ostrea lurida
qPCR
RNA
'SR ID: 1504'
'SR ID: 1505'
Ran qPCRs on the O.lurida total RNA I isolated on 20150507 to assess presence of gDNA carryover with Oly Actin primers (SR IDs: 1505, 1504).
May 12, 2015
Sam White
 

qPCR - Jake O.lurida ctenidia RNA (Control Samples) From 20150507

2015
actin
ctenidia
gill
olympia oyster
Opticon2
Ostrea lurida
qPCR
RNA
'SR ID: 1504'
'SR ID: 1505'
Ran qPCRs on the O.lurida total RNA I isolated on 20150507 to assess presence of gDNA carryover with Oly Actin primers (SR IDs: 1505, 1504).
May 12, 2015
Sam White
 

RNA Isolation – Geoduck Gonad in Paraffin Histology Blocks

2015
Protein expression profiles during sexual maturation in Geoduck
DNased RNA
geoduck
gonad
histology cassettes
NanoDrop1000
Panopea generosa
paraffin
PAXgene Tissue RNA Kit
RNA
RNA isolation
RNA quantification
UPDATE 20150528: The RNA isolated in this notebook entry may have been consolidated on 20150528.
May 7, 2015
Sam White
 

RNA Isolation – Jake’s O. lurida Ctenidia Control from 20150422

2015
ctenidia
gill
heat shock
NanoDrop1000
olympia oyster
Ostrea lurida
RNA
RNA isolation
RNA quantification
RNAzol RT
Isolated RNA from Jake’s Olympia oyster ctenidia, controls, collected on 20150422. Samples had been homogenized and stored @ -80C.
May 7, 2015
Sam White
 

Bioinformatics - Trimmomatic/FASTQC on C.gigas Larvae OA NGS Data

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
bioinformatics
BS-seq
Crassostrea gigas
FASTQC
graphs
ipython notebook
jupyter notebook
Pacific oyster
Trimmomatic
troubleshooting
In another troubleshooting attempt for this problematic BS-seq Illumina data, I’m going to use Trimmomatic to remove the first 39 bases of each read. This is due to the fact…
May 6, 2015
Sam White
 

RNA Isolation - Jake's O. lurida Ctenidia 1hr Heat Stress from 20150422

2015
ctenidia
DEPC-H2O
gill
heat shock
NanoDrop1000
olympia oyster
Ostrea lurida
pics
RNA isolation
RNA quantification
RNAzol RT
Isolated RNA from Jake’s Olympia oyster ctenidia, 1hr heat shock, collected on 20150422. Samples had been homogenized and stored @ -80C.
May 6, 2015
Sam White
 

RNA Isolation – Geoduck Gonad in Paraffin Histology Blocks

2015
Protein expression profiles during sexual maturation in Geoduck
geoduck
histology cassettes
NanoDrop1000
Panopea generosa
paraffin
PAXgene Tissue RNA Kit
RNA isolation
RNA quantification
UPDATE 20150528: The RNA isolated in this notebook entry may have been consolidated on 20150528.
May 5, 2015
Sam White
 

BLAST - C.gigas Larvae OA Illumina Data Against GenBank nt DB

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
bioinformatics
BLAST
BLASTn
BS-seq
Crassostrea gigas
GenBank
ipython notebook
jupyter notebook
NCBI
Pacific oyster
In an attempt to figure out what’s going on with the Illumina data we recently received for these samples, I BLASTed the 400ppm data set that had previously been de-novo asse…
May 4, 2015
Sam White
 

Goals - May 2015

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
Goals
Lineage-specific DNA methylation patterns in developing oysters
LSU C.virginica Oil Spill MBD BS Sequencing
Protein expression profiles during sexual maturation in Geoduck
BS-seq
Crassostrea gigas
Crassostrea virginica
Eastern oyster
geoduck
Pacific oyster
Panopea generosa
Here are the things I plan to tackle throughout the month of May:
May 1, 2015
Sam White
 

BLASTN - C.gigas OA Larvae to C.gigas Ensembl 1.24 BLAST DB

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
BLAST
Crassostrea gigas
ipython notebook
jupyter notebook
Pacific oyster
In an attempt to figure out what’s going on with the Illumina data we recently received for these samples, I BLASTed the 400ppm data set that had previously been de-novo asse…
Apr 29, 2015
Sam White
 

RNA Isolation – Geoduck Gonad in Paraffin Histology Blocks

2015
Protein expression profiles during sexual maturation in Geoduck
geoduck
gonad
histology cassettes
Panopea generosa
paraffin
PAXgene Tissue RNA Kit
RNA isolation
RNA quantification
UPDATE 20150528: The RNA isolated in this notebook entry may have been consolidated on 20150528.
Apr 26, 2015
Sam White
 

Bioanalyzer Data - Geoduck RNA from Histology Blocks

2015
Protein expression profiles during sexual maturation in Geoduck
bioanalyzer
electropherogram
foot
gel
geoduck
Panopea generosa
RNA
RNA Pico
I received the Bioanalyzer data back for the geoduck foot RNA samples I submitted 20150422. The two samples were run on the RNA Pico chip assay.
Apr 24, 2015
Sam White
 

RNA Isolation – Geoduck Gonad in Paraffin Histology Blocks

2015
Protein expression profiles during sexual maturation in Geoduck
DNased RNA
geoduck
gonad
histology cassettes
NanoDrop1000
Panopea generosa
PAXgene Tissue RNA Kit
RNA isolation
RNA quantification
UPDATE 20150528: The RNA isolated in this notebook entry may have been consolidated on 20150528.
Apr 23, 2015
Sam White
 

Bioanalyzer Submission - Geoduck Gonad RNA from Histology Blocks

2015
Protein expression profiles during sexual maturation in Geoduck
bioanalyzer
geoduck
gonad
Panopea generosa
paraffin
RNA
Submitted 3μL (~75ng) of RNA from each of the two gonad samples isolated from foot tissue embedded in paraffin histology blocks 20150409 (to assess quality of RNA) to Jesse…
Apr 22, 2015
Sam White
 

Quality Trimming - C.gigas Larvae OA BS-Seq Data

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
bioinformatics
BS-seq
Crassostrea gigas
FASTQC
ipython notebook
jupyter notebook
larvae
OA
ocean acidification
Pacific oyster
Trimmomatic
Jupyter (IPython) Notebook: 20150414_C_gigas_Larvae_OA_Trimmomatic_FASTQC.ipynb
Apr 15, 2015
Sam White
 

Quality Trimming - LSU C.virginica Oil Spill MBD BS-Seq Data

2015
LSU C.virginica Oil Spill MBD BS Sequencing
BS-seq
Crassostrea virginica
Eastern oyster
FASTQC
ipython notebook
jupyter notebook
MBD-Seq
NGS sequencing
oil
Trimmomatic
Jupyter (IPython) Notebook: 20150414_C_virginica_LSU_Oil_Spill_Trimmomatic_FASTQC.ipynb
Apr 15, 2015
Sam White
 

Sequence Data Analysis - LSU C.virginica Oil Spill MBD BS-Seq Data

2015
LSU C.virginica Oil Spill MBD BS Sequencing
BS-seq
Crassostrea virginica
Eastern oyster
FASTQC
LSU
MBD-Seq
NGS sequencing
oil
Performed some rudimentary data analysis on the new, demultiplexed data downloaded earlier today:
Apr 13, 2015
Sam White
 

Sequence Data Analysis - C.gigas Larvae OA BS-Seq Data

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
BS-seq
Crassostrea gigas
FASTQC
larvae
NGS sequencing
OA
ocean acidification
Pacific oyster
Compared total amount of data generated from each index. The commands below send the output of the ‘ls -l’ command to awk. Awk sums the file sizes, found in the 5th field…
Apr 13, 2015
Sam White
 

Sequence Data - C.gigas OA Larvae BS-Seq Demultiplexed

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
BS-seq
Crassostrea gigas
larvae
NGS sequencing
OA
ocean acidification
Pacific oyster
I had previously contacted Doug Turnbull at the Univ. of Oregon Genomics Core Facility for help demultiplexing this data, as it was initially returned to us as a single data…
Apr 13, 2015
Sam White
 

Sequence Data - LSU C.virginica Oil Spill MBD BS-Seq Demultiplexed

2015
LSU C.virginica Oil Spill MBD BS Sequencing
BS-seq
Crassostrea virginica
Eastern oyster
LSU
MBD-Seq
NGS sequencing
oil
I had previously contacted Doug Turnbull at the Univ. of Oregon Genomics Core Facility for help demultiplexing this data, as it was initially returned to us as a single data…
Apr 13, 2015
Sam White
 

RNA Isolation - Geoduck Gonad in Paraffin Histology Blocks

2015
Protein expression profiles during sexual maturation in Geoduck
Disruptor Genie
geoduck
gonad
histology
histology cassettes
NanoDrop1000
Panopea generosa
paraffin
PAXgene Tissue RNA Kit
RNA isolation
RNA quantification
Isolated RNA from geoduck gonad previously preserved with the PAXgene Tissue Fixative and Stabilizer and then embedded in paraffin blocks. See Grace’s notebook for full…
Apr 8, 2015
Sam White
 

Sequencing Data - C.gigas Larvae OA

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
BS-seq
checksum
code
Crassostrea gigas
curl
HiSeq2500
larvae
md5
OA
ocean acidification
Pacific oyster
Our sequencing data (Illumina HiSeq2500, 100SE) for this project has completed by Univ. of Oregon Genomics Core Facility(order number 2212).
Mar 19, 2015
Sam White
 

Epinext Adaptor 1 Counts - LSU C.virginica Oil Spill Samples

2015
LSU C.virginica Oil Spill MBD BS Sequencing
Before contacting the Univ. of Oregon facility for help with this sequence demultiplexing dilemma, I contacted Epigentek to find out what the other adaptor sequence that is…
Mar 17, 2015
Sam White
 

TruSeq Adaptor Counts – LSU C.virginica Oil Spill Sequences

2015
LSU C.virginica Oil Spill MBD BS Sequencing
Initial analysis, comparing barcode identification methods, revealed the following info about demultiplexing on untrimmed sequences:
Mar 16, 2015
Sam White
 

TruSeq Adaptor Identification Method Comparison - LSU C.virginica Oil Spill Sequences

2015
LSU C.virginica Oil Spill MBD BS Sequencing
barcodes
Crassostrea virginica
Eastern oyster
FASTQ
FASTQC
fastx_barcode_splitter
grep
index sequences
ipython notebook
jupyter notebook
TruSeq
We recently received Illumina HiSeq2500 data back from this project. Initially looking at the data, something seems off.  Using FASTQC, the quality drops of drastically…
Mar 14, 2015
Sam White
 

DNA Quantification - Claire's C.gigas Sheared DNA

2015
Lineage-specific DNA methylation patterns in developing oysters
Crassostrea gigas
DNA Quantification
heat shock
Pacific oyster
Quant-iT DNA BR Kit
In an attempt to obtain the most accurate measurement of Claire’s sheared, heat shock mantle DNA, I quantified the samples using a third method: fluorescence.
Mar 3, 2015
Sam White
 

Library Quality Assessment - C.gigas OA larvae Illumina libraries

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
bioanalyzer
BS-seq
Crassostrea gigas
EpiNext Post-Bisulfite DNA Library Preparation Kit
Genomics Core Facility
larvae
library prep
OA
ocean acidification
Pacific oyster
University of Oregon
Ran the 400ppm library preps on a DNA1000 Assay Chip (Agilent) on the Agilent 2100 Bioanalyzer.
Mar 2, 2015
Sam White
 

BS-seq Library Prep - C.gigas Larvae OA 1000ppm

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
bisulfite conversion
BS-seq
Crassostrea gigas
EpiNext Post-Bisulfite DNA Library Preparation Kit
larvae
library prep
Methylamp DNA Modification
NanoDrop1000
OA
ocean acidification
Pacific oyster
Pooled 200ng each of the sheared 1B1 (4μL) & 1B2 (used the entire sample, 20μL) 5.13.11 1000ppm C.gigas larvae DNA samples for a total of 400ng. Total volume = 24μL.
Feb 27, 2015
Sam White
 

DNA Quantification - C.gigas Larvae 1000ppm

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
Crassostrea gigas
DNA
larvae
NanoDrop1000
OA
ocean acidification
Pacific oyster
After the discovery that there wasn’t any DNA in the BS-seq Illumina library prep and no DNA in the bisulfite-treated DNA pool, I decided to try to recover any residual DNA…
Feb 26, 2015
Sam White
 

DNA Quantification - Claire's Sheared C.gigas Mantle Heat Shock Samples

2015
Lineage-specific DNA methylation patterns in developing oysters
Crassostrea gigas
DNA Quantification
graphs
heat shock
mantle
NanoDrop1000
Pacific oyster
I previously checked Claire’s sheared DNA on the Bioanalyzer to verify the fragment size and to quantify the samples. Looking at her notebook, her numbers differ greatly…
Feb 26, 2015
Sam White
 

Bioanalyzer - C.gigas Sheared DNA from 20140108

2015
Lineage-specific DNA methylation patterns in developing oysters
bioanalyzer
Crassostrea gigas
DNA
DNA1000
electropherogram
heat shock
mantle
Pacific oyster
spreadsheet
To complement MBD ChiP-seq data and RNA-seq data that we have from this experiment, we want to generate, at a minimum, some BS-seq data from the same C.gigas individuals…
Feb 20, 2015
Sam White
 

Library Prep - Quantification of C.gigas larvae OA 1000ppm library

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
BS-seq
Crassostrea gigas
DNA Quantification
FLx800 plate reader
larvae
library prep
OA
ocean acidification
Pacific oyster
Quant-iT DNA BR Kit
The completed BS Illumina library made on Friday (1000ppm) was quantified via fluorescence using the Quant-iT DNA BR Kit (Life Technologies/Invitrogen).  Also quantified Jake…
Feb 9, 2015
Sam White
 

Sequencing Data - LSU C.virginica MBD BS-Seq

2015
LSU C.virginica Oil Spill MBD BS Sequencing
BS-seq
checksum
code
Crassostrea virginica
curl
Eastern oyster
HiSeq2500
LSU
MBD
md5
oil
Data Received
Our sequencing data (Illumina HiSeq2500, 100SE) for this project has completed by Univ. of Oregon Genomics Core Facility (order number 2112).
Feb 9, 2015
Sam White
 

Bisulfite NGS Library Prep - Bisulfite Conversion & Illumina Library Construction of C.gigas larvae DNA

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
bisulfite conversion
BS-seq
Crassostrea gigas
DNA
larvae
library prep
OA
ocean acidification
Pacific oyster
The previous attempt at constructing a library for the 1000ppm larvae samples failed. I had previously sheared, quantified, and concentrated the DNA from this sample. As I…
Feb 6, 2015
Sam White
 

Bisuflite NGS Library Prep – C.gigas larvae OA bisulfite library quantification

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
BS-seq
Crassostrea gigas
DNA Quantification
FLx800 plate reader
library prep
OA
ocean acidification
Pacific oyster
Quant-iT DNA BR Kit
The two completed BS Illumina libraries (400ppm and 1000ppm) were quantified via fluorescence using the Quant-iT DNA BR Kit (Life Technologies/Invitrogen).  Used 1uL of …
Jan 28, 2015
Sam White
 

Bisuflite NGS Library Prep - C.gigas larvae OA bisulfite DNA (continued from yesterday)

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
barcodes
BS-seq
Crassostrea gigas
library prep
Pacific oyster
Continued Illumina library prep of bisulfite-treated DNA samples (400ppm and 1000ppm; from 20150115) with Methylamp DNA Modification Kit (Epigentek) (PDF). Performed bead…
Jan 27, 2015
Sam White
 

Bisuflite NGS Library Prep - C.gigas larvae OA bisulfite DNA

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
Crassostrea gigas
larvae
library prep
Methylamp DNA Modification
OA
ocean acidification
Pacific oyster
The two pooled bisulfite-treated DNA samples (400ppm and 1000ppm) from 20150115 were used to prepare bisulfite Illumina libraries with EpiNext Post-Bisulfite DNA Library…
Jan 26, 2015
Sam White
 

Library Cleanup - LSU C.virginica MBD BS Library

2015
LSU C.virginica Oil Spill MBD BS Sequencing
bioanalyzer
Crassostrea virginica
DNA Quantification
Eastern oyster
electropherogram
library prep
I was contacted by the sequencing facility at the University of Oregon regarding a sample quality issue with our library.  As evidenced by the electropherogram below, there…
Jan 22, 2015
Sam White
 

DNA Bisulfite Conversion - C.gigas larvae OA Sheared DNA

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
bisulfite conversion
DNA
After discussing with Steven, decided to use only samples from 20110513, due to high algae amounts present in the 20110519 samples.
Jan 14, 2015
Sam White
 

SpeedVac - C.gigas larvae OA DNA

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
concentrate
Crassostrea gigas
DNA
SpeedVac
The DNA extracted and sheared on 20150109 was in a volume too great to proceed with bisulfite conversion.  Dried the samples to complete dryness in a SpeedVac (~4hrs). …
Jan 12, 2015
Sam White
 

DNA Isolation - C.gigas larvae from 2011 NOAA OA Experiment

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
Crassostrea gigas
DNA Isolation
DNA Quantification
DNA Shearing
larvae
OA
ocean acidification
Some tubes contained a high quantity of algae, based on quantity of material in tube and overall green color.
Jan 9, 2015
Sam White
 

Bisulfite NGS Library - LSU C.virginica Oil Spill MBD Bisulfite DNA Sequencing Submission

2014
LSU C.virginica Oil Spill MBD BS Sequencing
Combined the following libraries in equal quantities (17ng each) to create a single, multiplexed sample for sequencing (LSU_Oil_01):
Dec 22, 2014
Sam White
 

Bisulfite NGS Library Prep - LSU C.virginica Oil Spill MBD Bisulfite DNA and Emma's C.gigas Larvae OA Bisulfite DNA (continued from yesterday)

2014
Crassostrea gigas larvae OA (2011) bisulfite sequencing
LSU C.virginica Oil Spill MBD BS Sequencing
Continued library prep from yesterday. Set up Library Amplification according to the protocol. The samples received the following Barcode Indices:
Dec 18, 2014
Sam White
 

Bisulfite NGS Library Prep - LSU C.virginica Oil Spill Bisulfite DNA and Emma's C.gigas Larvae OA Bisulfite DNA

2014
Crassostrea gigas larvae OA (2011) bisulfite sequencing
LSU C.virginica Oil Spill MBD BS Sequencing
Constructed next generation libraries (Illumina) using the bisulfite-treated DNA from yesterday using the EpiNext Post-Bisulfite DNA Library Preparation Kit - Illumina…
Dec 17, 2014
Sam White
 

Bisulfite Conversion - LSU C.virginica Oil Spill MBD DNA and Emma's C.gigas Larvae OA DNA

2014
Crassostrea gigas larvae OA (2011) bisulfite sequencing
LSU C.virginica Oil Spill MBD BS Sequencing
Performed bisulfite conversion on MBD DNA samples from LSU C.virginica oil spill samples (see 201411202 and 20141126) and Emma’s C.gigas larvae OA DNA samples (see 20141121)…
Dec 16, 2014
Sam White
 

DNA Isolation - Claire's C.gigas Female Gonad for Illumina Bisulfite Sequencing

2014
Lineage-specific DNA methylation patterns in developing oysters
Due to poor “tag counts” from the initial sequencing (DATE) and the re-sequencing (20131127) of this sample, the HTGU facility has concluded that the library is probably at…
Dec 11, 2014
Sam White
 

EtOH Precipitation - LSU C.virginica Oil Spill MBD Continued (from 20141126)

2014
LSU C.virginica Oil Spill MBD BS Sequencing
Precipitation was continued according to the MethylMiner Methylated DNA Enrichment Kit (Invitrogen). Since I will need sample volumes of 24uL for the subsequent bisulfite…
Dec 2, 2014
Sam White
 

Methylated DNA Enrichment (MBD) - LSU C.virginica Oil Spill gDNA

2014
LSU C.virginica Oil Spill MBD BS Sequencing
Enrichment was performed using the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) according to the manufacturer’s protocol with the following changes:
Nov 26, 2014
Sam White
 

DNA Shearing - LSU C.virginica Oil Spill gDNA

2014
LSU C.virginica Oil Spill MBD BS Sequencing
Used the remainder of the “sheared” samples (see today’s earlier entry; ~2750ng). Brought the volumes up to 80uL and transferred to 0.5mL snap cap tubes. The volume of 80uL…
Nov 25, 2014
Sam White
 

Gel - Sheared gDNA

2014
LSU C.virginica Oil Spill MBD BS Sequencing
Ran ~250ng (out of 3000ng, according to Claire) of LSU C.virginica oil spill gDNA on a gel that was previously sheared by Claire to verify that shearing was successful.
Nov 25, 2014
Sam White
 

RNA Seq - C.gigas Total RNA from Claire's Pre/Post Heat Shock

2014
Samples Submitted
Shipped (dry ice) ~15ug of total RNA from each of the following samples to Genewiz, Inc for high throughput transcriptomic sequencing (Illumina HiSeq2500, 100bp, single end).
Nov 24, 2014
Sam White
 

DNA Isolation - C.gigas Larvae from Emma OA Experiments

2014
Crassostrea gigas larvae OA (2011) bisulfite sequencing
Isolated gDNA using DNazol from the following larval samples for potential MBD selection and bisulfite sequencing:
Nov 21, 2014
Sam White
 

RAD Sequencing - Oly Oyster gDNA-01 RAD Library (from 20141110)

2014
Olympia oyster reciprocal transplant
Samples Submitted
library prep
olympia oyster
Ostrea lurida
RAD-seq
Prepared 10nM of the library in total volume of 20uL of Buffer EB (Qiagen) + 0.1% Tween-20, according the University of Oregon’s Genomic’s Core.
Nov 17, 2014
Sam White
 

DNA Quantification - Oly Oyster gDNA-01 RAD Library

2014
Olympia oyster reciprocal transplant
Quantified the library using the Quant-It BR Kit (Life Technologies) according to the manufacturer’s protocol. Only used 1uL of the RAD library due to the small volume (15uL).
Nov 10, 2014
Sam White
 

Library Prep - Oly Oyster gDNA-01 RAD

2014
Olympia oyster reciprocal transplant
Used gel-purified, size-selected DNA from yesterday to prepare the RAD library using the Kappa LTP Kit:
Nov 7, 2014
Sam White
 

DNA Shearing & Size Selection - Oly Oyster gDNA RAD P1 Adapters (from 20141105)

2014
Olympia oyster reciprocal transplant
Pooled “low quality” samples and pooled “high quality” samples separately (in 1.5mL snap cap tubes) prior to shearing to improve chances of getting similar DNA size ranges.
Nov 6, 2014
Sam White
 

Ligation - Illumina P1 Adapters for Oly Oyster gDNA-01 RAD Sequencing (from 20141031)

2014
Olympia oyster reciprocal transplant
Made 25nM working stock from the 100nM stock adapter plate provided by Carita. Added 2uL of each adapter to corresponding well of SbfI digested DNA (e.g. DNA plate well A1…
Nov 5, 2014
Sam White
 

Restriction Digest - Oly Oyster gDNA-01 for RAD Sequencing (from 20141029)

2014
Olympia oyster reciprocal transplant
Samples required two days of drying for all samples to fully dry down.
Oct 31, 2014
Sam White
 

DNA Allocation - Oly Oyster gDNA-01 for RAD Sequencing (from 20141022)

2014
Olympia oyster reciprocal transplant
Transferred 500ng of gDNA from each sample to a 96-well, low-profile, non-skirted PCR plate (sample layout matches that of the layout of the source gDNA plate) and air-dried…
Oct 29, 2014
Sam White
 

DNA Quantification - Oly Oyster gDNA-01 for RAD Sequencing (from 20141014)

2014
Olympia oyster reciprocal transplant
Quantified the gDNA isolated 20141014 using the Quant-iT dsDNA Broad Range kit (Life Technologies).
Oct 22, 2014
Sam White
 

DNA Isolation - Olympia Oyster Populations for RAD Sequencing

2014
Olympia oyster reciprocal transplant
Olympia oysters from three different Puget Sound locations/populations (HL, NF, and SN) were collected and stored @ -80C on 8/29/2103.
Oct 14, 2014
Sam White
 

Package - Received Package from Jerome LaPeyre from LSU

2014
LSU C.virginica Oil Spill MBD BS Sequencing
Oyster (C.virginica) gill samples exposed to “no oil” and “highest level of oil.” Samples were stored in Rack #2 in the -80C. Images of the box label and included paperwork…
Sep 26, 2014
Sam White
 

DNA Isolation - C.gigas Larvae from Katie Latterhos

2014
Miscellaneous
Since the previous isolation attempt was unsuccessful (see 20140922), we’re trying a slightly different approach than yesterday.
Sep 23, 2014
Sam White
 

DNA Isolation - C.gigas Larvae from Katie Latterhos and Emma

2014
Miscellaneous
Isolated gDNA from two C.gigas larvae samples (stored in RNA Later) from Katie Latterhos:
Sep 22, 2014
Sam White
 

PCR - Mac's Bisulfite-Treated DNA

2014
Miscellaneous
Realized that the PCR performed on 20140828 used the incorrect forward primer! As such, am repeating as before, but with the correct forward primer:
Sep 3, 2014
Sam White
 

PCR - Mac's Bisulfite-Treated DNA

2014
Miscellaneous
Per Mac’s request, ran a PCR on a set of bisulfite-treated DNA (in her gDNA 2014 box in small -20C):
Aug 28, 2014
Sam White
 

RNA-Seq - Sea Star Data Download

2014
Sea star RNA-seq
Received RNA-seq data from Cornell. They provided a convenient download script for retrieving all the data files at one time (a bash script containing a series of wget…
May 28, 2014
Sam White
 

RNA Isolation - Jessica's Geoduck Larval Stages

2014
Miscellaneous
Isolated RNA from the following samples provided by Jessica Blanchette (stored in RNA later):
May 27, 2014
Sam White
 

DNA Isolation - Mackenzie's C.gigas EE2 Gonad Samples

2014
Miscellaneous
Isolated DNA from the following samples, provided by Mackenzie:
May 16, 2014
Sam White
 

Sample Submission - Colleen Sea Star (Pycnopodia) Coelomycete RNA for Illumina Sequencing

2014
Samples Submitted
Sea star RNA-seq
Sent the following samples (in their entirety) to Cornell for Illumina HiSeq 100bp paired-end sequencing:
May 14, 2014
Sam White
 

RNA Isolation - Colleen Sea Star (Pycnopodia) Coelomycete Sample

2014
Sea star RNA-seq
Apparently the Bio26 sample provided on 20140428 was incorrect. Instead, the sample should have been CF26.
May 8, 2014
Sam White
 

RNA Isolation - Colleen Sea Star (Pycnopodia) Coelomycete Samples

2014
Sea star RNA-seq
Isolated RNA from the following samples (provided by Colleen Burge):
Apr 28, 2014
Sam White
 

DNA Isolation - Claire's C.gigas Female Gonad

2014
Lineage-specific DNA methylation patterns in developing oysters
Trying this sample again(!!), but will now use TE for pellet resuspension to prevent sample degradation. Incubated sample RT on rotator in 500uL of DNazol + 2.7uL of…
Apr 25, 2014
Sam White
 

Ethanol Precipitation - Colleen's Sea Star Coelomycete RNA from Yesterday

2014
Sea star RNA-seq
Performed an EtOH precipitation on the sea start RNA due to some residual column resin (?) in the tubes after elution.
Apr 25, 2014
Sam White
 

RNA Clean Up - Colleen's Sea Star Coelomycete RNA from 20140416

2014
Sea star RNA-seq
Zymoresearch support suggested putting the samples through another set of columns to help clean up the apparent phenol carryover that was seen (absorbance peak shifted to…
Apr 24, 2014
Sam White
 

RNA Isolation - Colleens' Sea Star Coelomycetes Samples

2014
Sea star RNA-seq
Isolated RNA from the following samples stored in RNAlater:
Apr 16, 2014
Sam White
 

DNA Isolation - Test Sample

2014
Lineage-specific DNA methylation patterns in developing oysters
Miscellaneous
Due to the recent poor quality gDNA that has been isolated from C.gigas gonad, I decided to do a quick test using TE for DNA pellet resuspension in hopes that old Buffer EB…
Apr 16, 2014
Sam White
 

Phenol-Chloroform DNA Clean Up - Mac and Claire's Samples (from 20140410)

2014
Lineage-specific DNA methylation patterns in developing oysters
Due to low 260/230 values and Mac’s smeary sample, performed a phenol-chloroform DNA cleanup on the samples isolated 20140410.
Apr 14, 2014
Sam White
 

RNA Isolation - Sea Star Coelomocytes (from Colleen)

2014
Sea star RNA-seq
Isolated RNA from two samples stored in RNAlater that had either no visible pellet or a minutely visible pellet:
Apr 10, 2014
Sam White
 

DNA Isolation - Claire's C.gigas Female Gonad and Mac's C.gigas Gonad

2014
Lineage-specific DNA methylation patterns in developing oysters
Due to the poor quality DNA yielded by the DNeasy Kit (Qiagen; see 20140404), I am re-isolating these samples using DNazol (Molecular Research Center). Weighed tissue from…
Apr 10, 2014
Sam White
 

Cloned Hard Drive - Windows XP Opticon Computer (Aquacul8)

2014
Computer Servicing
Cloned the XP hard drive of the computer hooked up to the Opticon qPCR machine using Macrium Reflect Free. Verified that the clone is bootable and operates correctly. Will…
Apr 4, 2014
Sam White
 

DNA gel - Claire's C.gigas Female Gonad and Mac's C.gigas Gonad

2014
Lineage-specific DNA methylation patterns in developing oysters
Ran out 2uL of Clair’es C.gigas female gonad gDNA (from 20140328) and Mac’s C.gigas gonad gDNA (from 20140402) for quality assessment. Both samples had been isolated using…
Apr 4, 2014
Sam White
 

RNA Isolation - Sea Star Coelomocytes (provided by Colleen Burge)

2014
Sea star RNA-seq
Tried another method of RNA Isolation for comparison with regular TriReagent method.
Apr 2, 2014
Sam White
 

RNA Isolation - Sea Star Coelomocytes (provided by Colleen Burge)

2014
Sea star RNA-seq
Isolated RNA from the following samples (stored in RNAlater):
Apr 1, 2014
Sam White
 

DNA Isolation - Mackenzie's C.gigas Gonad Sample

2014
Miscellaneous
Mac’s been having some difficulty getting good quality gDNA from some of her gonad samples, so she asked me to give it a shot.
Apr 1, 2014
Sam White
 

DNA Isolation - C.gigas Female Gonads (from frozen)

2014
Lineage-specific DNA methylation patterns in developing oysters
Isolated gDNA from Claire’s “Female DNA” (from 05/16/2013) using the Qiagen Blood & Tissue DNeasy Kit according to the manufacturer’s protocol, with the following changes:
Mar 28, 2014
Sam White
 

DNA Quality Check - Yanouk's Oyster gDNA

2014
Miscellaneous
We’ve had some Illumina sequencing issues with Yanouk’s samples, so I ran the samples out on a 0.8% agarose gel to evaluate the levels of degradation. Loaded 2uL of each…
Mar 14, 2014
Sam White
 

DNA Isolation - Geoduck

2014
Miscellaneous
Isolated additional geoduck gDNA from the two fresh (now frozen) geoduck’s that Brent provided me with on 20140212 so that we can potentially isolate RNA from the same…
Feb 19, 2014
Sam White
 

DNA Precipitation - Geoduck DNA from 20140213

2014
Miscellaneous
After speaking with Axa regarding the DNA concentrations, he would like the DNA from the ethanol-fixed tissue to be more concentrated, and he wants them in ddH2O instead of…
Feb 18, 2014
Sam White
 

DNA Isolation - Geoduck

2014
Miscellaneous
Since yesterday’s DNA isolation failed to yield sufficient quantity of DNA from the ethanol-fixed samples, I isolated additional DNA from the same samples.
Feb 13, 2014
Sam White
 

DNA Isolation - Geoduck

2014
Miscellaneous
Isolated gDNA from 6 geoduck siphon samples provided by Brent using the Qiagen DNeasy Spin Kit. Samples were as follows:
Feb 12, 2014
Sam White
 

Gylcogen Assay - Emma's C.gigas Whole Body Samples (continued from yesterday)

2013
Miscellaneous
Samples from yesterday were centrifuged 30mins, 4000g, 4C (fixed angle rotor).
Dec 7, 2013
Sam White
 

Gylcogen Assay - Emma's C.gigas Whole Body Samples

2013
Miscellaneous
Finally located the remaining half of Emma’s samples. These had already been freeze dried AND pulverized! So, I just had to weigh out ~half of each sample for the glycogen…
Dec 6, 2013
Sam White
 

Gylcogen & Carboyhydrate Assays - Emma's C.gigas Whole Body Samples (continued from yesterday)

2013
Miscellaneous
Samples from yesterday were centrifuged 30mins, 4000g, 4C (fixed angle rotor).
Nov 26, 2013
Sam White
 

Gylcogen and Carboyhydrate Assays - Emma's C.gigas Whole Body Samples

2013
Miscellaneous
Samples were previously freeze dried overnight and stored @ -20C. To maximize sample homogeneity and, thus, increase accuracy of both assays, all samples were mechanically…
Nov 25, 2013
Sam White
 

PCR - Lake Trout C1q

2013
Miscellaneous
Repeated PCR from 20130919, but with a newly designed reverse primer. Primers were designed using MethPrimer (SR IDs: 1553, 1555). Primers were designed using MethPrimer:
Oct 28, 2013
Sam White
 

PCR - Lake Trout C1q

2013
Miscellaneous
Repeated PCR from 20130919, but with a newly designed set of primers that targets the desired region of C1q for sequencing (SR IDs: 1553, 1554). Primers were designed in…
Oct 10, 2013
Sam White
 

DNA Quantification - Yanouk's DNA Samples

2013
Miscellaneous
Oct 4, 2013
Sam White
 

PCR - Lake Trout C1q

2013
Miscellaneous
Ran PCR on lake trout DNA and lake trout bisulfite-converted DNA. Used primers SRIDs: 1551 and 1552. DNA was isolated by Caroline Storer on 4/4/2011 and bisulfite converted…
Sep 19, 2013
Sam White
 

PCR - Hexokinase Partial CDS

2013
Miscellaneous
Performed PCR using the primers CG_HK_CDS_2132-2158 (SRID: 1521) and Cg_Hk_CDS_3’_no_stop (SRID: 1519) on pooled C.gigas cDNA (from DATE).
Apr 9, 2013
Sam White
 

PCR - Hexokinase and Partial Exon #1

2013
Miscellaneous
Performed PCR using newly designed primers to amplify the C. gigas hexokinase “promoter” (-2059bp from start) along with a portion of the first exon.
Apr 8, 2013
Sam White
 

PCR - Hexokinase Promoter and CDS (repeat from 20130227)

2013
Miscellaneous
Performed a repeat of the failed PCR from 20130227, but used a pool of cDNA (made from 20110311 C.gigas cDNA) instead of a single sample and changed the annealing temp to 50C.
Mar 14, 2013
Sam White
 

PCR - Hexokinase Promoter and CDS

2013
Miscellaneous
Performed PCR to amplify the C.gigas hexokinase (ACCESSION#) promoter region (-2059bp) and the CDS without the stop codon. Elimination of the stop codon allows for…
Feb 27, 2013
Sam White
 

Reverse Transcription - Herring RNA from 20091026

2013
Miscellaneous
Performed an RT reaction on pooled herring gonad and liver mRNA from 20091026 for James Raymond at the UNLV. A single RT reaction was performed using 12.75uL (208ng) of the…
Feb 13, 2013
Sam White
 

qPCR - Halley cDNA Check

2012
Miscellaneous
Ran qPCR on Halley’s cDNA to see if I could get them to work. She has been getting high levels of fluorescence at the initiation of the qPCR cycling that shouldn’t be there. …
Nov 28, 2012
Sam White
 

Reverse Transcription - FISH441 RNA

2012
Miscellaneous
Reverse transcribed the class FISH441 RNA to cDNA. Followed protocol provided on the FISH441 Wiki page, NOT the usual Roberts Lab protocol, with some modifications.
Nov 21, 2012
Sam White
 

qPCR - Manila Clam Larvae cDNA (from August 2012 - Dave's Notebook)

2012
Miscellaneous
Ran qPCR on manila clam larvae cDNA that Dave made on 8/7/2012, using the sample sets from 7/29/2011 and 8/5/2011 of the OA manila clam experiment he ran.
Nov 8, 2012
Sam White
 

qPCR - Manila Clam Larvae cDNA (from August 2012 - Dave's Notebook)

2012
Miscellaneous
Ran qPCR on manila clam larvae cDNA that Dave made on 8/7/2012, using the sample sets from 7/29/2011 and 8/5/2011 of the OA manila clam experiment he ran.
Nov 8, 2012
Sam White
 

qPCR - Manila Clam Larvae cDNA (from August 2012 - Dave's Notebook)

2012
Miscellaneous
Ran qPCR on manila clam larvae cDNA that Dave made on 8/7/2012, using the sample sets from 7/29/2011 and 8/5/2011 of the OA manila clam experiment he ran.
Nov 8, 2012
Sam White
 

qPCR - DNased Manila Clam Larvae RNA (from August 2012 - Dave's Notebook)

2012
Miscellaneous
Performed qPCR on Dave’s manila clam larvae DNased RNA from August 2012 using EF1a primers (SR IDs: 1463, 1474).
Oct 26, 2012
Sam White
 

Received oysters from Taylor Shellfish.

2012
Miscellaneous
Photos of oysters are here:
Oct 16, 2012
Sam White
 

qPCR - Opticon Test

2012
Miscellaneous
Ran qPCR to test uniformity of Opticon 2, after it was serviced on 20120926.
Oct 10, 2012
Sam White
 

Minipreps - Emma's Illumina Library Cloning

2012
Miscellaneous
Performed plasmid isolation on 17 bacterial cultures Emma inoculated yesterday using the QIAprep Spin Mini Kit (Qiagen) using ~1.4mL of culture according to the…
Jul 23, 2012
Sam White
 

Illumina RNAseq Library Construction - 32 C.gigas Individuals

2012
Crassostrea gigas
Illumina
library prep
Pacific oyster
RNA-seq
Took heat-fragmented RNA provided by Emma (see Emma’s Notebook, 7/3/2011) and proceeded to make first strand cDNA, as described in the Eli Meyer protocol for Illumina HiSeq . …
Jul 11, 2012
Sam White
 

Oligo Reconstitution - Illumina RNAseq Library Oligos and Barcodes

2012
Miscellaneous
Reconstituted all of the oligos and barcodes for library construction in TE (pH = 8.0) to a final concentration of 100uM. Created 10uM working stocks of all oligos and…
Jul 11, 2012
Sam White
 

Chloroform Clean Up - Lexie's QPX RNA from 20110504

2012
Miscellaneous
After submission of QPX samples to HTGU for Illumina library prep yesterday, I was notified that there was insufficient RNA for the QPX RNA samples. I checked the source RNA…
Jul 10, 2012
Sam White
 

Sample Submission - QPX RNA and DNA for Illumina 36bp single-end RNA/DNAseq

2012
Miscellaneous
Samples Submitted
Submitted samples to HTGU for Illumina sequencing.
Jul 9, 2012
Sam White
 

QPX Sample Pooling for Illumina Sequencing

2012
Miscellaneous
Pooling volumes/quantities for QPX RNA/DNA-seq: 20120705 Oly larvae and QPX HiSeq Calcs
Jul 6, 2012
Sam White
 

qPCR - Detection of V.tubiashii Presence and Expression Using VtpA Primers in DNA/cDNA from yesterday

2012
Miscellaneous
Ran qPCR with VtpA primers on cDNA and DNA (from yesterday) of C.gigas larvae to see levels of V.tubiashii compared to their water filter samples (see 20120326). Master mix…
May 1, 2012
Sam White
 

Reverse Transcription - DNased C.gigas Larval RNA from 20120427

2012
Miscellaneous
M-MLV
reverse transcription
RNA
Vibrio tubiashii
Performed reverse transcription using random primers (Promega) diluted 1:100 (5ng/uL) with 175ng of DNased total RNA. Random primers were used because we will be targeting…
Apr 30, 2012
Sam White
 

qPCR - Check DNased RNA from Earlier Today for Residual gDNA

2012
CFX96
Crassostrea gigas
DNased RNA
larvae
Pacific oyster
qPCR
Vibrio tubiashii
VtpA
Ran qPCR using V.tubiashii VtpA primers (from Elene; no SR ID). Used 0.5uL of each DNased RNA sample, which equals ~40ng of RNA, which would be the equivalent amount of RNA…
Apr 27, 2012
Sam White
 

DNase Treatment - C.gigas Larvae RNA from yesterday

2012
Miscellaneous
Treated 5ug of total RNA (in a 50uL rxn) using Turbo DNA-free (Ambion) according to the “Standard” protocol. Samples were spec’d on the Roberts Lab NanoDrop 1000.
Apr 27, 2012
Sam White
 

gDNA Isolation - C.gigas Larvae from Taylor Summer 2011

2012
Miscellaneous
Samples that had been split from earlier today (see the RNA Isolation below) were resuspended in 1mL of DNAzol (MRC). 100ug of Proteinase K (Fermentas) was added to each…
Apr 26, 2012
Sam White
 

RNA Isolation - C.gigas Larvae from Taylor Summer 2011

2012
Miscellaneous
Samples had been stored in RNA Later (Ambion). Samples were pelleted and the RNA Later supe removed. Samples were washed (2x) with 1mL TE (pH = 8.0) to remove excess salt…
Apr 26, 2012
Sam White
 

qPCR - Taylor Water Filter DNA Extracts from 20120322 - Sam White

2012
Miscellaneous
Ran qPCR on the Taylor water filter DNA extracts from 20120322 using V.tubiashii VtpA primers (provide by Elene; no SR ID?) instead of 16s primers, which failed to produce…
Mar 26, 2012
Sam White
 

qPCR - Repeat of qPCR from Earlier Today

2012
Miscellaneous
Repeated exactly what was done earlier today due to apparent contamination in negative controls.
Mar 23, 2012
Sam White
 

qPCR - Taylor Water Filter DNA Extracts from Yesterday

2012
Miscellaneous
Ran qPCR on the Taylor water filter DNA extracts from yesterday using V.tubiashii 16s primers (SR IDs: 455, 456). Used RE22 DNA as a positive control, provided by Elene. Mast…
Mar 23, 2012
Sam White
 

DNA Extraction - Taylor Water Filter Samples from 2011

2012
Miscellaneous
Extracted DNA from the following water filter samples using the Qiagen DNeasy Blood & Tissue Kit:
Mar 22, 2012
Sam White
 

Reverse Transcription - Dave's Manila Clam (Venerupis philippinarum) DNased RNA from 20120307 and 20120302

2012
Miscellaneous
Performed reverse transcription on 1.5ug of DNased RNA in a 75uL reaction, using oligo dT primers. All reagents were scaled appropriately (based on Promega’s M-MLV RT…
Mar 12, 2012
Sam White
 

qPCR - Dave's Manila Calm (Venerupis philippinarum) DNased RNA from yesterday and 20120302

2012
Miscellaneous
Performed qPCR on all DNased RNA samples from this group (samples #1-48) using beta actin primers (SR IDs: 1379, 1380). 0.5uL of each DNased RNA was used, which was the…
Mar 8, 2012
Sam White
 

RNA Isolation - Dave's Manila Clam (Venerupis philippinarum) Gill Samples (#25-48)

2012
Miscellaneous
Isolated RNA from Manila Clam gill samples provided by Dave, according to protocol. Samples were resuspended in 0.1%-DEPC H2O and spec’d on the Roberts Lab NanoDrop1000.…
Mar 7, 2012
Sam White
 

DNase - Dave's Manila Clam (Venerupis philippinarum) Gill RNA from Yesterday

2012
Miscellaneous
DNased RNA using Ambion’s Turbo DNA-free Kit following the “routine” protocol. 5ug of total RNA from each sample was treated in 50uL reactions. Samples will be spec’d on…
Mar 2, 2012
Sam White
 

RNA Isolation - Dave's Manila Clam (Venerupis philippinarum) Gill Samples (#1-24)

2012
Miscellaneous
Isolated RNA from Manila Clam gill samples provided by Dave according to protocol. Samples were resuspended in 0.1%-DEPC H2O and spec’d on the Roberts Lab NanoDrop1000.…
Mar 1, 2012
Sam White
 

qPCR - cDNA from 20120208

2012
Miscellaneous
Performed qPCR on all 12 samples. Used the following primers, provided by Elene, to detect V.tubiashii expression:
Feb 9, 2012
Sam White
 

qPCR - cDNA from earlier today

2012
Miscellaneous
Performed qPCR on all 12 samples. Used Cg_EF1aF/R2 (SR IDs: 1410 & 1412) for one set of qPCRs and Vtub_16s_F/R (SR IDs: 455 & 456) for the other set of qPCRs. Used pooled…
Feb 8, 2012
Sam White
 

Reverse Transcription - C.gigas larvae DNased RNA (from 20120125)

2012
Miscellaneous
Performed reverse transcription on Dnased RNA from 20120125 using 175ng RNA from each sample. Also used random primers (instead of the usual Oligo dT primers) since these…
Feb 8, 2012
Sam White
 

qPCR - DNased RNA from earlier today

2012
Miscellaneous
Checked DNased RNA samples from earlier today for the presence of residual gDNA. Used C.gigas BB16 gDNA (from 20110201) diluted to ~7ng/uL as a positive control to match the…
Jan 25, 2012
Sam White
 

DNAse - C.gigas RNA from 20120124

2012
Miscellaneous
5ug of each RNA was DNased using Ambion’s Turbo DNA-free Kit, according to the rigorous protocol and spec’d on Roberts Lab NanoDrop 1000. RNA volume calcs are here.
Jan 25, 2012
Sam White
 

RNA Isolation - C.gigas Larvae from 20110412 & 20110705 (Continued from 20120112)

2012
Miscellaneous
All of the RNA samples were re-combined with their respective counterparts and subject to a standard EtOH precipitation (0.1 volumes of 3M NaOAc, pH = 5.2, 2.5 volumes 100%…
Jan 24, 2012
Sam White
 

RNA Isolation - C.gigas Larvae from 20110412 & 20110705

2012
Miscellaneous
RNA was isolated from C.gigas larvae collected from Taylor Shellfish hatchery on the dates noted above. Samples were in RNA Later. RNA Later was removed. Attempted…
Jan 12, 2012
Sam White
 

Sequencing - COX/PGS Clones from yesterday/today

2011
Miscellaneous
Samples were submitted for sequencing to the University of Washington HTGU, two times from each direction using vector M13F/R primers. See Sequence Log for plate layout.
Oct 14, 2011
Sam White
 

Mini-preps - COX/PGS Cloning Colonies from today

2011
Miscellaneous
Selected 10 colonies (1-8, 18, 28) for mini-preps. Inoculated 5mL 1x LB + 50ug/mL of Kanamycin. Incubated O/N, 37C, 200RPM. 3mL of each culture were used for mini-preps.…
Oct 13, 2011
Sam White
 

PCR - COX/PGS Cloning Colony Screens from yesterday

2011
Miscellaneous
Performed PCR on 40 colonies using both qPCR primer sets to see if I could differentiate between which colonies potentially contained each isoform to reduce the amount of…
Oct 13, 2011
Sam White
 

Cloning - Purified COX/PGS "qPCR Fragment" from 20111006

2011
Miscellaneous
Cloned the purified “qPCR Fragment” from 20111006 using the TOPO TA Cloning Kit (Invitrogen). Performed a half reaction (total volume = 3uL), using 1uL of purified PCR…
Oct 12, 2011
Sam White
 

PCR - Purified COX/PGS 1/2 DNA from earlier today

2011
Miscellaneous
Ran PCR using primers Cg_COX1/2_qPCR_F, Cg_COX1_qPCR_R, Cg_COX2_454align1_R (SR IDs: 1192, 1191, 1190; respectively). Template was pooled cDNA from 20110311 of various…
Oct 6, 2011
Sam White
 

PCR - Region Outside of COX/PGS qPCR Primers

2011
Miscellaneous
Ran PCR using primers Cg_COX_982_F and Cg_COX_2138_R (SR IDs: 1149 & 1151, respectively). Template was pooled cDNA from 20110311 of various C.gigas tissues. These primers…
Oct 6, 2011
Sam White
 

Ethanol Precipitation - Full-length PGS1 cDNA (from 20110921)

2011
Miscellaneous
Performed an EtOH on gel-purified PCR products from 20110921. Briefly, added 0.1 vols of 3M sodium acetate (pH=5.2; 43uL), mixed and then added 2.5 vols of 100% EtOH…
Sep 29, 2011
Sam White
 

PCR - Full-length PGS1 cDNA

2011
Miscellaneous
Still have insufficient quantities of DNA for sequencing. Master mix calcs and cycling params are here. Additionally, used some of the purified PCR product as template in…
Sep 21, 2011
Sam White
 

Ethanol Precipitation - Purified PGS1 PCR from yesterday

2011
Miscellaneous
Added 0.1 vols of 3M sodium acetate (pH = 5.2; 38uL) and 2 vols of 100% EtOH (836uL). Incubated 30mins @ -20C. Pelleted DNA 16,000g, 15mins, 4C. Removed supe. Washed pellet…
Sep 21, 2011
Sam White
 

PCR - Full-length PGS1 cDNA

2011
Miscellaneous
Need more PCR product for sequencing. Repeated reaction from 20110825.
Sep 20, 2011
Sam White
 

PCR - Full-length PGS2 cDNA

2011
Miscellaneous
Repeated PCR from 20110825 to attempt to amplify the full-length cDNA for PGS2 (COX2), however this time using a more robust polymerase (Amplitaq Gold) in hopes of getting…
Sep 14, 2011
Sam White
 

PCR - Full-length PGS1 & PGS2 cDNAs

2011
Miscellaneous
Ran PCR to amplify full-length cDNAs of PGS1 & PGS2 (COX1 & COX2) using primers designed to anneal in the 5’/3’UTRs of each isoform. PGS1 primers = SRIDs: 1377, 1378. PGS2…
Aug 25, 2011
Sam White
 

qPCR - C.gigas V.vulnificus Exposure cDNA (from 20110311)

2011
cDNA
CFX96
Crassostrea gigas
defensin
GAPDH
Pacific oyster
qPCR
Vibrio exposure
Vibrio vulnificus
Ran a qPCR using 3hr Vibrio vulnificus exposure cDNA from 20110311. Original experiment conducted on 20110111 with defensin primers (SR IDs: 1109 & 1070) and GAPDH (SR IDs…
Aug 11, 2011
Sam White
 

Sequencing - C.gigas COX2/PGS2 Clone #4 from 20110728

2011
Miscellaneous
Used new primers for sequencing (SR IDs: 1351 & 1352) clone #4. Sequenced clone two times in each direction. DNA and primers were sent for sequencing at ASU. Requested “High…
Aug 4, 2011
Sam White
 

Plasmid Isolation & Sequencing - C.gigas COX2/PGS2 Clones (from yesterday)

2011
Miscellaneous
Isolated plasmid DNA from 3mL of liquid cultures that were inoculated yesterday using Qiagen’s miniprep kit. DNA was eluted with 50uL of EB. DNA was prepped and sent for…
Jul 28, 2011
Sam White
 

Bacterial Cultures - C.gigas COX2/PGS2 Clones (from yesterday)

2011
Miscellaneous
Inoculated 4 x 5mL 1xLB + Kan50 with a colony from each set of clones, incubated 37C, 200RPM, O/N. Will mini prep and send for sequencing tomorrow.
Jul 27, 2011
Sam White
 

Colony PCRs - C.gigas COX2/PGS2 Clones (from yesterday)

2011
Miscellaneous
Performed colony PCRs on the 4 sets of cloning reactions that were performed yesterday using the M13F/R vector primers. Colonies were picked, restreaked on a fresh LB Kan50…
Jul 26, 2011
Sam White
 

Cloning - C.gigas COX2/PGS2 5'/3' RACE Products (from earlier today)

2011
Miscellaneous
The bands that were excised and purified earlier today were cloned in to pCR2.1 using the TOPO TA Cloning Kit (Invitrogen) according to the manufacturer’s protocol with the…
Jul 25, 2011
Sam White
 

5'/3' RACE - C.gigas COX2/PGS2 Nested RACE PCR

2011
Miscellaneous
Performed nested RACE PCR on the RACE PCR products generated on 20110722 using the following nested primers: PGS2_ngspRACE_5’ (SR ID: 1350) and PGS2_ngspRACE_3’ (SR ID…
Jul 25, 2011
Sam White
 

5'/3' RACE - C.gigas COX2/PGS2 RACE PCR

2011
Miscellaneous
Additional RACE using gene specific primers (SR IDs: 1347 & 1348) for C.gigas COX2/PGS2 according to Clontech’s SMARTer cDNA RACE Kit protocol. 3’/5’ RACE cDNA libraries are…
Jul 22, 2011
Sam White
 

Sequencing - PGS Hi 4 (PGS2/COX2)

2011
Miscellaneous
Sent plasmid prep to ASU (5uL of plasmid + 1uL of 10uM M13F/R). SJW01 = M13F, SJW02 = M13R.
Jul 15, 2011
Sam White
 

Plasmid Isolation - Miniprep on PGS Hi 4 Colony from yesterday

2011
Miscellaneous
Plasmid was isolated from 3mL of liquid culture started yesterday using the Qiagen MiniPrep Kit, according to the manufacturer’s protocol. Will send off for sequencing.
Jul 12, 2011
Sam White
 

PCR - Colony PCR on Restreaked PGS2 Clones from 20110707

2011
Miscellaneous
Ran a colony PCR at the same time that I inoculated liquid cultures, using M13 primers.
Jul 11, 2011
Sam White
 

Bacterial Cultures - Liquid Cultures of PGS2/COX2 Colonies from 20110707

2011
Miscellaneous
Inoculated 5mL of 1xLB + Kan50 with re-streaked colonies from 20110707. Incubated O/N, 37C, 200RPM. Will isolated plasmids of those with inserts tomorrow.
Jul 11, 2011
Sam White
 

Clone Restreaking - PGS2 Hi/Lo Clones (from 20110421)

2011
Miscellaneous
Sequencing of the PGS2/COX2 clone failed (was empty vector). Restreaked bacterial clones on to a Kan50 plate (made 20110413 by SJW) from a plate that Caroline Storer had…
Jul 7, 2011
Sam White
 

qPCR - C.gigas GAPDH second rep on V.vulnificus exposure cDNA (from 20110311) and standard curves for COX1, COX2, GAPDH

2011
Miscellaneous
Ran a qPCR on all cDNA samples. Created a standard curve to possibly allow for use of the BioRad software for gene expression analysis. Standard curve was created from…
Jun 3, 2011
Sam White
 

qPCR - C.gigas actin and GAPDH on V.vulnificus exposure cDNA (from 20110311)

2011
Miscellaneous
Ran a qPCR on all cDNA samples from the V.vulnificus exposure experiment from 20110111. This qPCR was to test 2 of 4 potential normalizing genes to evaluate which genes show…
Jun 2, 2011
Sam White
 

qPCR - C.gigas 18s and EF1a on V.vulnificus exposure cDNA (from 20110311)

2011
Miscellaneous
Ran a qPCR on all cDNA samples from the V.vulnificus exposure experiment from 20110111. This qPCR was to test 2 of 4 potential normalizing genes to evaluate which genes show…
Jun 2, 2011
Sam White
 

qPCR - C.gigas COX2 on V.vulnificus exposure cDNA (from 20110311)

2011
Miscellaneous
Ran a qPCR on all cDNA samples from the V.vulnificus exposure experiment from 20110111. Primers used were Cg_COX1/2_qPCR_F (SR ID: 1192) & Cg_COX2_454align1_R (SR ID: 1190).…
Jun 1, 2011
Sam White
 

qPCR - C.gigas COX1 on V.vulnificus exposure cDNA (from 20110311)

2011
Miscellaneous
Ran a qPCR on all cDNA samples from the V.vulnificus exposure experiment from 20110111. Primers used were Cg_COX1/2_qPCR_F (SR ID: 1192) & Cg_COX1_qPCR_R (SR ID: 1191).…
Jun 1, 2011
Sam White
 

qPCR - Hard Clam NGS Primer Checks

2011
Miscellaneous
Ran a qPCR to evaluate a large batch of primers (40 sets) that were ordered per Steven, based off of the most recent SOLiD run (samples submitted 3/10/2011; see Dave’s…
May 23, 2011
Sam White
 

qPCR - Lexie's QPX Temp & Tissue Experiment (see Lexies Notebook 4/26/2011)

2011
Miscellaneous
Ran qPCR with Lexie’s cDNA samples from this experiment with the following primer sets in order to better evaluate her biological reps:
May 20, 2011
Sam White
 

qPCR - Emma's New 3KDSqPCR Primers

2011
Miscellaneous
Due to previous contamination issues with Emma’s primers, Emma asked me to order new primers, reconstitute them and run a qPCR for her to see if we could eliminate her…
May 20, 2011
Sam White
 

Reverse Transcription - Hard Clam Gill DNased RNA (from 20110509)

2011
Miscellaneous
Performed reverse transcription on DNased RNA from the hard clam vibrio tubiashii challenge experiment (see Dave’s Notebook 5/2/2011), following the Promega M-MLV RT…
May 11, 2011
Sam White
 

DNase - Hard Clam Gill RNA (from earlier today)

2011
Miscellaneous
DNased 5ug of RNA from each sample with Ambion’s Turbo DNA-free Kit, according to the manufacturer’s rigorous protocol. Samples were spec’d and stored @ -80C in the “Hard…
May 9, 2011
Sam White
 

RNA Isolation - Hard Clam Gill Tissue from Vibrio Experiment (see Dave's Notebook 5/2/2011)

2011
Miscellaneous
Isolated RNA in 1mL of Tri-Reagent according to the manufacturer’s protocol. Also, finished RNA isolation of samples that were started 20110506. Samples were resuspended in…
May 9, 2011
Sam White
 

Primer Design - Hard Clam NGS Primers

2011
Miscellaneous
Hard clam
Mercenaria mercenaria
primers
Designed primers for 40 PCR targets derived from the most recent SOLiD data by Steven(Evernote link) using BatchPrimer3. BatchPrimer3 results are here.
May 8, 2011
Sam White
 

RNA Isolation - Hard Clam Gill Tissue from Vibrio Experiment (see Dave's Notebook 5/2/2011)

2011
Miscellaneous
Isolated RNA in 1mL of Tri-Reagent according to manufacturer’s protocol. Samples were precipitated with isopropanol and stored over the weekend @ -20C. Will conclude…
May 6, 2011
Sam White
 

Received - Live Hard Clams From Scott Lindell

2011
Miscellaneous
Received two bags containing ~24 live clams (didn’t count) in each bag. One bag labeled as “Mashpee Control” and the other “BX Selected.” Clams were stored @ 4C by Steven.
Apr 28, 2011
Sam White
 

Bacterial Cultures - Colonies Selected from Yesterday's Colony PCRs

2011
Miscellaneous
Inoculated 5mL of 1x LB + Kan50 (made by Steven on 3/23/11). Incubated O/N at 37C, 250RPM. Will perform mini preps tomorrow. The following samples were selected:
Apr 26, 2011
Sam White
 

Mini Preps - Liquid Cultures from yesterday

2011
Miscellaneous
Mini prepped 3mLs of each culture, according to Qiagen protocol. Samples were eluted with 50uL of Buffer EB.
Apr 26, 2011
Sam White
 

Bacterial Cultures - Colonies Selected by Steven from Steven's Re-Streaked Plate

2011
Miscellaneous
Inoculated 5mL of 1x LB + Kan50 (made by Steven on 3/23/11). Incubated O/N @ 37C, 250RPM. Will perform mini preps tomorrow. The following samples were selected (red text on…
Apr 25, 2011
Sam White
 

Colony PCR - Colonies from COX1 Genomic Cloning (from 20110411)

2011
Miscellaneous
Ran colony PCR on various colonies produced from cloning on 20110411. All colonies were picked, re-streaked on Kan50 plate(s) and PCR’d. Master mix calcs are here. Cycling…
Apr 25, 2011
Sam White
 

Colony PCR - 5'RACE Colony: COX2 (repeat of yesterday's PCR)

2011
Miscellaneous
Repeated yesterday’s PCR on the re-streaked colony in order to run the product on a gel with a more appropriate ladder. See yesterday’s entry for all PCR info.
Apr 22, 2011
Sam White
 

Colony PCR - 5' RACE Colony: COX2

2011
Miscellaneous
One white colony (marked with arrow in image linked) from the two plates from Steven’s cloning (from yesterday) was picked, restreaked on a new Kan50 plate (no X-gal) and…
Apr 21, 2011
Sam White
 

Colony PCR - 5' RACE Colonies

2011
Miscellaneous
Two light blue colonies (there were no white colonies) were picked, restreaked on a new Kan50 plate (no X-gal) and PCR’d.
Apr 14, 2011
Sam White
 

Ligations - COX1/COX2 PCR Products

2011
Miscellaneous
Performed ligations/cloning on a variety of COX1 genomic and COX 5’ RACE products using the TOPO TA Cloning Kit (Invitrogen). Used 2uL of gel-purified PCR product in each…
Apr 11, 2011
Sam White
 

5'/3' RACE PCRs - Nested PCRs for COX2 Sequence

2011
Miscellaneous
Due to the failure of the primary PCR on both 5’ and 3’ RACE cDNA libraries (from 20080619) yesterday, will perform nested PCR using a nested GSP designed by Steven…
Apr 7, 2011
Sam White
 

5'/3' RACE PCRs - COX2 Sequence on 5' & 3' RACE Libraries (from 20080619)

2011
Miscellaneous
Ran PCRs on both the 5’ & 3’ RACE libraries created 20080619 with a new COX2 gene-specifc (GSP) primer designed by Steven (CgPGSRACEsrGSP1; SR ID: 1208). Although this…
Apr 6, 2011
Sam White
 

qPCR - C.gigas BB/DH cDNA for PROPS (TIMP3(BB) primers)

2011
PROPS
Performed qPCR using cDNA from 20110311. This was performed for 2 reps with TIMP3(BB) (SR IDs: 1067 & 1106). Master mix calcs are here. Plate layout, cycling params, etc.…
Mar 21, 2011
Sam White
 

qPCR - C.gigas BB/DH cDNA for PROPS (HMGP primers)

2011
PROPS
Performed qPCR using cDNA from 20110311. This was performed for 2 reps with HMGP (SR IDs:359 & 360). Master mix calcs are here. Plate layout, cycling params, etc can be…
Mar 21, 2011
Sam White
 

qPCR - C.gigas COX1/COX2 Tissue Distribution

2011
Miscellaneous
Performed qPCR using pooled cDNA from 20110311. Pooled 2uL from each of the following samples groups: Dg 3hr C, Gill 1hr C, Gill 1hr E, Mantle 3hr C, and Muscle 3hr C. Master…
Mar 15, 2011
Sam White
 

qPCR - C.gigas BB/DH cDNA for PROPS

2011
PROPS
Performed qPCR using cDNA from 20110311. This was performed for additional reps for TIMP3(BB) (SR IDs:1067 & 1106) and HMGP (SR IDs:359 & 360). Master mix calcs are here.…
Mar 14, 2011
Sam White
 

Reverse Transcription - C.gigas BB/DH DNased RNA (from 20090507) for PROPS

2011
PROPS
Performed RT on DNased RNA using Promega MMLV RT and Oligo dT according to manufacturer’s protocol, using 1ug of DNased RNA, but in a 50uL reaction. Due to large number of…
Mar 11, 2011
Sam White
 

Reverse Transcription - C.gigas DNased RNA (from 20110131) from V.vulnificus Exposure & Tissues (from 20110111)

2011
Miscellaneous
Performed RT on DNased RNA using Promega MMLV RT and Oligo dT according to manufacturer’s protocol, using 1ug of DNased RNA. Due to large number of samples, cDNA was made in…
Mar 11, 2011
Sam White
 

SOLiD Sequencing Submission

2011
Miscellaneous
Submitted the following 8 samples for SOLiD sequencing at HTGU:
Mar 10, 2011
Sam White
 

mRNA Isolation - Pooled Black Abalone Dg RNA (from Abalone Dg Exp 1)

2011
Miscellaneous
mRNA was isolated for SOLiD sequencing by HTGU. Made two pools of San Nick RNA (Control and Exposed) using equal amounts (5ug) of each individual sample. Individual samples…
Mar 7, 2011
Sam White
 

3'RACE - C.gigas 3'RACE for COX2

2011
Miscellaneous
Used Cg_COX2_3’RACE_short (SR ID: 1197) & Cg_COX2_3’RACE_long (SR ID: 1196) and the Clonetech SMART RACE cDNA Amplification Kit (unknown acquisition date) to attempt to…
Mar 4, 2011
Sam White
 

NanoDrop1000 Comparison - Roberts vs. Young Lab

2011
Miscellaneous
A previous comparison was performed (see 20110209), but it was determined that the standard DNA being used to test the machines was old/degraded. Lisa ordered a new standard…
Mar 1, 2011
Sam White
 

qPCR - Check DNased RNA BB01 for Residual gDNA (from earlier today)

2011
PROPS
Ran qPCR on DNased RNA from earlier today to verify removal of contaminating gDNA. Used C.gigas 18s primers (SR IDs: 156, 157). 0.5uL (~40ng) of DNased RNA was used for…
Mar 1, 2011
Sam White
 

DNase - C.gigas BB01 (PROPS) RNA (from 20090507)

2011
PROPS
Since the previous DNase treatment failed for this sample, will repeat but will start with less RNA (5ug instead of 10ug). Need more DNased RNA to finish repeating of PROPS.…
Mar 1, 2011
Sam White
 

qPCR - Check DNased RNA BB01 for Residual gDNA (from earlier today)

2011
PROPS
Ran qPCR on DNased RNA from earlier today to verify removal of contaminating gDNA. Used C.gigas 18s primers (SR IDs: 156, 157). 0.75uL (~50ng) of DNased RNA was used for…
Feb 28, 2011
Sam White
 

DNase - C.gigas BB01 from 20110225

2011
PROPS
Used EtOH precipitated BB01 RNA from 20110225 and followed Ambion’s “rigorous” protocol, utilizing a total of 2uL of DNAse. Briefly, samples were incubated @ 37C for 30mins…
Feb 28, 2011
Sam White
 

Ethanol Precpitation - DNased RNA BB01 (from earlier today)

2011
PROPS
Due to residual gDNA contamination, will EtOH precipitate in order to treat with DNase again. Add 0.5 vols 3M NaAOc (pH=
Feb 25, 2011
Sam White
 

qPCR - Check DNased RNA BB01 for Residual gDNA (from earlier today)

2011
PROPS
Ran qPCR on DNased RNA from earlier today to verify removal of contaminating gDNA. Used C.gigas 18s primers (SR IDs: 156, 157). 0.5uL (50ng) of DNased RNA was used for…
Feb 25, 2011
Sam White
 

DNase - C.gigas BB01 from 20110216

2011
PROPS
Used EtOH precipitated BB01 RNA from 20110216 and followed Ambion’s “rigorous” protocol, utilizing a total of 2uL of DNAse. Briefly, samples were incubated @ 37C for 30mins…
Feb 25, 2011
Sam White
 

Ethanol Precipitation - DNased RNA BB01 (from earlier today)

2011
PROPS
Due to residual gDNA contamination, will EtOH precipitate in order to treat with DNase again. Add 0.5 vols 3M NaAOc (pH = 5.2), 2.5 vols 100% EtOH, mixed and incubated @…
Feb 16, 2011
Sam White
 

qPCR - Check DNased RNA BB01 & 09 (from earlier today)

2011
PROPS
Ran qPCR on DNased RNA from earlier today to verify that it was free of contaminating gDNA. Used C.gigas 18s primers (SR IDs: 156, 157). 0.5uL (50ng) of DNased RNA was used…
Feb 16, 2011
Sam White
 

DNase - C.gigas BB/DH (PROPS) RNA (from 20090507)

2011
PROPS
Need more DNased RNA to finish repeating of PROPS. Some samples had insufficient quantities of DNased RNA remaining in BB01 and BB09. Used 10ug of each RNA and followed…
Feb 16, 2011
Sam White
 

Data Analysis - Young Lab ABI 7300 Calibration Checks

2011
Miscellaneous
All runs (3 runs were conducted) were created using a master mix containing C.gigas gDNA (either 50ng or 100ng), 1X Promega qPCR Master Mix, 0.2uM each of forward/reverse…
Feb 9, 2011
Sam White
 

qPCR - Test Young Lab qPCR Calibration

2011
Miscellaneous
This is a repeat of the two runs from yesterday, just to see if there is a correlation between the failed plates being the first of the day or not. Master mix calcs and…
Feb 9, 2011
Sam White
 

NanoDrop1000 Comparison - Roberts vs. Young Lab

2011
Miscellaneous
Due to an apparent reduction in assay sensitivity for the Hematodidium qPCR assay, we have decided to determine if the spec readings of the plasmid DNA being used for the…
Feb 9, 2011
Sam White
 

qPCR - Test Young Lab qPCR Calibration (Repeat)

2011
Miscellaneous
This was repeated from earlier today due to the failure of the previous run, but had to use new gDNA since I ran out of the stock I had previously used. Master mix calcs and…
Feb 8, 2011
Sam White
 

PCR - New C. gigas COX Primers for Sequencing of Isoforms

2011
Miscellaneous
Used new primers for obtaining bands for additional sequencing of both COX isoforms in C. gigas. Master mix calcs are here. Master mix shorthand (MM##) is described below:
Feb 8, 2011
Sam White
 

qPCR - Test Young Lab qPCR Calibration (Repeat)

2011
Miscellaneous
This is a repeat of a run from 20110204. Here’re master mix calcs. This was being repeated to evaluate whether or not the relative differences in Ct values observed on…
Feb 8, 2011
Sam White
 

qPCR - Test Young Lab qPCR Calibration (Repeat)

2011
Miscellaneous
This is a repeat of an earlier run from today, but with a different qPCR plate. [Here’re master mix calcs (bottom half of…
Feb 4, 2011
Sam White
 

qPCR - Test Young Lab qPCR Calibration

2011
Miscellaneous
Recently, the Young Lab’s ABI 7300 qPCR machine was calibrated. Steven asked me to run a plate and see how well the calibration worked. Ran a plate with C.gigas gDNA and…
Feb 4, 2011
Sam White
 

Genomic PCR - Repeat of C.gigas COX genomic PCR from 20110118

2011
Miscellaneous
This was repeated to generate more PCR product for sequencing purposes. PCR master mix calcs and cycling params are here. Master mixes 04 and 05 (MM04 and MM05) were…
Jan 31, 2011
Sam White
 

DNase - DNase C.gigas RNA from 20110120, 20110121 and 20110124

2011
Miscellaneous
5ug of RNA was DNased using Ambion’s Turbo DNA-free kit, following the rigorous protocol (0.5uL of DNase for 30 mins then additional 0.5uL of DNase for 30mins). Calcs for…
Jan 28, 2011
Sam White
 

RNA Isolation - Various C.gigas Tissue from 20110111

2011
Miscellaneous
RNA was isolated in 1mL TriReagent, according to protocol. Samples were resuspended in 50uL 0.1% DEPC-H2O and spec’d. RNA was stored @ -80C in “Shellfish RNA Box #4
Jan 24, 2011
Sam White
 

RNA Isolation - Various C.gigas Tissue from 20110111

2011
Miscellaneous
RNA was isolated in 1mL TriReagent, according to protocol. Samples were resuspended in 50uL 0.1% DEPC-H2O and spec’d. RNA was stored @ -80C in “Shellfish RNA Box #4”.
Jan 21, 2011
Sam White
 

RNA Isolation - Various C.gigas Tissue from 20110111

2011
Miscellaneous
RNA was isolated in 1mL TriReagent, according to protocol. Samples were resuspended in 50uL 0.1% DEPC-H2O and spec’d. RNA was stored @ -80C in “Shellfish RNA Box #4”.
Jan 20, 2011
Sam White
 

Genomic PCR - C.gigas cyclooxygenase (COX) genomic sequence

2011
Miscellaneous
Attempt to obtain full genomic sequence for C.gigas COX. PCR set up/cycling params/etc are here. Primer set combinations(master mixes) are as follows:
Jan 18, 2011
Sam White
 

Bacterial Dilutions - Determination of Colony Forming Units from Gigas Bacterial challenge (from earlier today)

2011
Miscellaneous
All dilutions were performed with 1x LB+ 1%NaCl. 100uL were plated of all dilutions (see below) on 1xLB+1%NaCL plates. Plates were incubated O/N @ 37C. Colonies will be…
Jan 11, 2011
Sam White
 

Gigas Bacterial Challenge - 1hr & 3hr Challenges with Vibrio vulnificus

2011
Miscellaneous
400mL O/N culture (1x LB+1% NaCl, 37C, 150RPM, 1L flask) of V.vulnificus (STRAIN??) and V.tubiashii (Strain: RE22) were pelleted (4300RPM, 25C, Sorvall ST-H750 rotor). Supe…
Jan 11, 2011
Sam White
 

SOLiD - Retrieved SOLiD Library Samples from CEG from 20101213

2010
Miscellaneous
Retrieved the following SOLiD libraries from the CEG and stored in -80C in the “NGS Libraries” Box.
Dec 23, 2010
Sam White
 

qPCR - COX qPCR Vibrio Exposure Response Check

2010
Miscellaneous
Used COX primers (SR IDs 1060, 1061) and cDNA from 20080327, which consisted of 7 control gigas gill and 7 vibrio-exposed (24hrs) gigas gill samples, labeled as C# and VE#…
Dec 13, 2010
Sam White
 

qPCR - COX qPCR Primer Test and Tissue Distribution

2010
Miscellaneous
Used new cyclooxygenase primers (SR IDs 1060, 1061) to see how they performed and to evaluate tissue distribution. Tissue distribution was evaluated using the following…
Dec 10, 2010
Sam White
 

Restriction Digestions/Ligations - MS-AFLP

2010
Miscellaneous
Reaction calculations are here. Samples were mixed and incubated @ 37C O/N (started at 6PM). Mac will take care of them tomorrow morning.
Nov 30, 2010
Sam White
 

Restriction Digestions - HpaII and MspI on Mac's C.gigas Samples: Round 1

2010
Miscellaneous
1st of 2 rounds of digests were performed. Calculations are here. Samples were incubated 37C for 3hrs, heat inactivated @ 80C for 30mins and then stored @ -20C.
Nov 29, 2010
Sam White
 

EtOH Precipitations - HpaII and MspI 2nd Round Digests from 20101124

2010
Miscellaneous
Samples were EtOH precipitated, according to protocol. Samples were resuspended in 20uL of Qiagen’s EB and spec’d.
Nov 29, 2010
Sam White
 

Restriction Digestions - HpaII and MspI on Mac's C.gigas Samples: Round 2

2010
Miscellaneous
Continued with 2nd round of digestions from yesterday. All samples were resuspended in 25uL of H2O yesterday, so brought volume up to 44uL with H2O, added 5uL of appropriate…
Nov 24, 2010
Sam White
 

Phenol:Chloroform Extractions and EtOH Precipitations - HapII and MspI digests from yesterday

2010
Miscellaneous
Restriction digests from yesterday were mixed with equal volume (50uL) of phenol:chloroform:IAA (25:24:1) and centrifuged 16,000g for 5mins @ 4C. Aqueous phase was…
Nov 23, 2010
Sam White
 

Restriction Digestions - HpaII and MspI on Mac's C.gigas gDNA Samples: Round 1

2010
Miscellaneous
Set up restriction digests for subsequent analysis by methylation specific PCR (MSP). This will be the first of two rounds of digestion with the same enzyme on each sample. S…
Nov 22, 2010
Sam White
 

QPX Washes

2010
Miscellaneous
Washed 4 day old QPX cultures. 3 isolates (S-1, TD-81, ATCC), two flasks (13mL) of each were washed in the following manner:
Oct 26, 2010
Sam White
 

gDNA Isolation

2010
Miscellaneous
Isolated gDNA from gray whale skin, human cheek cells (my own!) and two different species of algae (species 1, species 2) using Qiagen’s DNEasy Blood & Tissue Kit according…
Oct 26, 2010
Sam White
 

EtOH Precipitation - Whale gDNA from 20101022

2010
Miscellaneous
Precipitated whale gDNA in hopes of producing a sample with a higher concentration. Added 0.1 vols of 3M NaOAc (10uL), 2.5 vols of 100% EtOH (275uL), mixed thoroughly and…
Oct 25, 2010
Sam White
 

gDNA Isolation

2010
Miscellaneous
Isolated gDNA from crab (unknown species), starfish exposed to RoundUp (unknown species) and gray whale blubber using Qiagen’s DNEasy Kit, according to manufacturer’s…
Oct 22, 2010
Sam White
 

Received Hard Clam Samples and Live Clams from MBL

2010
Miscellaneous
Received 82 gill samples in RNA Later in 3 microfuge tube racks from MBL (Scott Lindell). Samples were catalogued, boxed (1 box) and stored at -80C.
Oct 19, 2010
Sam White
 

Received Hard Clam Samples from Rutgers

2010
Miscellaneous
30 gill tissue samples in RNA Later from CA, MA, & MAX each.
Oct 15, 2010
Sam White
 

qPCR - Test Plate for Opticon 2

2010
Miscellaneous
Ran a full plate for testing well-to-well consistency (or, inconsistency!) of the Opticon 2, since it’s been behaving poorly lately. This will provide us with an idea of…
Oct 12, 2010
Sam White
 

Opticon Calibration

2010
Miscellaneous
Distributed 50uL of FAM calibration dye to wells. Ran out of dye!!
Sep 17, 2010
Sam White
 

qPCR - Hard Clam Primers on cDNA from yesterday

2010
Miscellaneous
BigDef
C1qTNG
CA
CFX96
CytP450-like
ferritnin
graphs
GST
Hard clam
HemoDef
HSP 70
Immomix
lysozyme
MA
MAX
Mercenaria mercenaria
Mercenaria_Rel
metallothionein
Mm_TRAF6
NADHIV
qPCR
RACK1
SenescentProt
STI
SYTO 13
TfAP1
TLR
Performed qPCR on Friedman Lab machine targeting immune-related genes in hard clam. Rough plate layout/master mix calcs are here. qPCR report from Friedman Lab machine is here…
Sep 9, 2010
Sam White
 

Reverse Transcription - DNased Hard Clam RNA from earlier today

2010
Miscellaneous
Prepared cDNA using 1ug of RNA from each of the 3 pools (CA, MA, MAX) and processed according to Promega’s M-MLV protocol, using oligo dT primers. Calcs and master mix set…
Sep 8, 2010
Sam White
 

DNase - DNasing Hard Clam RNA from yesterday

2010
Miscellaneous
Pooled 2ug of each sample in each group (MAX, CA, MA) for a total of 6ug of RNA (3 total samples), brought volume up to 50uL and DNased using Ambion’s Turbo DNA-free…
Sep 8, 2010
Sam White
 

EtOH Precipitation - Hard Clam RNA from earlier today

2010
Miscellaneous
RNA was mixed with 0.1 vols of 3M NAOAc (pH = 5.2) and 2.5 vols of 100% EtOH, vortexed and incubated @ -20C for 30mins. RNA was pelleted @ 16,000g, 30mins, 4C. Supe was…
Sep 7, 2010
Sam White
 

RNA Isolation - Hard Clam Tissues Rec'd from Rutgers on 20100820

2010
Miscellaneous
RNA was isolated from the following samples using TriReagent, according to protocol:
Sep 7, 2010
Sam White
 

Package - Hard Clam Samples from MBL

2010
Miscellaneous
Rec’d package from Scott Lindell @ MBL containing 65 screw cap tubes in a white microtube rack. All tubes are tissues in RNA Later (presumably). One sample (MA4-5) was lost…
Sep 2, 2010
Sam White
 

Package - Hard Clam Samples from Rutgers

2010
Miscellaneous
Rec’d package of hard clam samples from Emily @ Rutgers on wet ice. Package contained numerous 1.5mL snap cap tubes separated in to groups in zip lock bags. Stored…
Aug 20, 2010
Sam White
 

qPCR - HpaII/MspI Digests from earlier today

2010
Miscellaneous
qPCR plate layout/setup is here.
Jul 9, 2010
Sam White
 

Restriction Digests - Various gigas gDNA from earlier today

2010
Miscellaneous
Digest master mixes are here. Digests were incubated @ 37C for 2hrs. and then heat inactivated @ 80C for 20mins.
Jul 9, 2010
Sam White
 

gDNA Isolation - Various gigas samples (continued from yesterday)

2010
Miscellaneous
Pelleted residual tissue 10mins @ 10,000g @ RT. Transferred supe to new tubes. Precipitated DNA with 0.25mL 100% EtOH. Incubated 3mins @ RT. DNA was pelleted 5mins @ 5000g @…
Jul 9, 2010
Sam White
 

gDNA Isolation - Various gigas samples

2010
Miscellaneous
Placed ~20mg fragments of tissue in 250uL DNAzol. Added 1.35uL of Proteinase K (Fermentas; 18.5mg/mL) to reach a final concentration of 100ug/mL. Incubated RT, O/N…
Jul 8, 2010
Sam White
 

MeDIP - SB/WB Fragmented gDNA EtOH precipitation (continued from 20100702)

2010
Miscellaneous
Finished EtOH precipitation of MeDIP gDNA. Samples were pelleted 16,000g, 4C, 30mins. Supe was discarded. Washed with 1mL 70% EtOH, pelleted 16,000g, 4C, 15mins. Supe…
Jul 8, 2010
Sam White
 

MeDIP - SB/WB Fragmented gDNA (continued from yesterday)

2010
Miscellaneous
Continued MeDIP process from yesterday. Protein A/G beads were pelleted XXXXXXXXX, supe transferred to clean tube. Beads were washed 3x in the following fashion, each wash…
Jul 2, 2010
Sam White
 

Restriction Digests - Various gigas gDNAs of Mac's

2010
Miscellaneous
Performed restriction digests. Made dilutions of all DNAs involved of 25ng/uL. Made enough for a total of 9 digests could be performed on each DNA. This allowed using 10uL…
Jul 2, 2010
Sam White
 

MeDIP - SB/WB Fragmented gDNA (continued from yesterday)

2010
Miscellaneous
Continued MeDIP process from yesterday. Added 20uL of Protein A/G Plus Agarose (Santa Cruz Biotech) beads to each sample and continued incubation with rotation @ 4C for…
Jul 1, 2010
Sam White
 

MeDIP - SB/WB Fragmented gDNA (from 20100625)

2010
Miscellaneous
After confirming proper fragmentation (~460bp average fragment size) via Bioanalyzer earlier today, began the MeDIP process. Brought fragmented DNA samples up to 350uL with…
Jun 30, 2010
Sam White
 

Bioanalyzer - Fragmented SB/WB gDNA (from 20100625)

2010
Miscellaneous
To gain a more quantitative assessment of the fragmentation from 20100625, I ran 1uL of each sample (~55ng, according to pre-fragmentation spec values) on the Agilent…
Jun 30, 2010
Sam White
 

gDNA Sonication - SB/WB gDNA pools (prep for MeDIP) from 20100618

2010
Miscellaneous
The previous attempt at sonication (see 20100618) failed, likely due to no using the correct equipment (tubes and Covaris adapter). The two gDNA pools, which had previously…
Jun 25, 2010
Sam White
 

Samples Received - Hard Clam samples from Rutgers and MBL

2010
Miscellaneous
Received sets of gill tissue and hemolymph in RNA Later from Rutgers (Emily). Here’s the note that was included with the samples.
Jun 24, 2010
Sam White
 

gDNA Sonication - SB/WB gDNA pools (prep for MeDIP) from earlier today

2010
Miscellaneous
The two gDNA pools (SB and WB) were sonicated using a Covaris S2. Used the guidelines of the manufacturer (listed below) for shearing gDNA to a desired target size (500bp):
Jun 18, 2010
Sam White
 

gDNA Precipitation - SB/WB gDNA pools (prep for MeDIP)

2010
Miscellaneous
8 gDNA samples from SB were pooled and 8 gDNA samples from WB were pooled, using equal amounts of gDNA from each sample (1250ng) for a total of 10ug (see SB/WB Mac’s MeDIP…
Jun 18, 2010
Sam White
 

gDNA Isolation - Mac gigas larvae samples: control larvae 6.7.10 and 5-aza tr larvae 6.7.10

2010
Miscellaneous
5-azacitidine
Crassostrea gigas
DNA Isolation
DNA Quantification
DNazol
gDNA
larvae
NanoDrop1000
Pacific oyster
Continued gDNA isolation of the above mentioned larvae samples that was started by Mac yesterday. Amount of larvae in tubes looked disproportionately large, relative to the…
Jun 8, 2010
Sam White
 

gDNA Isolation - Mac gigas gill samples (continued from yesterday)

2010
Miscellaneous
Crassostrea gigas
DNA Isolation
DNA Quantification
DNazol
gDNA
gel
gill
NanoDrop1000
Pacific oyster
R37
R51
RNAlater
Continued with gDNA isolation from yesterday’s samples. Samples were gently pipetted up and down to further dissolve remaining tissue, although tissue did not dissolve…
Jun 5, 2010
Sam White
 

gDNA Isolation - Mac gigas gill samples

2010
Miscellaneous
Crassostrea gigas
DNA Isolation
DNazol
gill
Pacific oyster
R37
R51
RNAlater
Set up gDNA isolation from the following samples:
Jun 4, 2010
Sam White
 

gDNA Isolation - Mac gigas gill samples (continued from yesterday)

2010
Miscellaneous
Continued with gDNA isolation from yesterday’s samples. Additionally, isolated gDNA from R51 01, but homogenized the tissue (using disposable 1.5mL mortar/pestle) in 0.5mL…
May 28, 2010
Sam White
 

Package Rec'd - From NOAA in Connecticut

2010
Miscellaneous
algae
Isochrysis sp. T-150
NOAA
package
Tetraselmis cheri Ply429
Thalassiaosira weissflugii TW
Rec’d 6 15mL conical tubes with liquid cultures of various algae. It appears that we rec’d two of each culture. No note/info included with package. Tubes will be stored @ RT…
May 27, 2010
Sam White
 

gDNA Isolation - Mac gigas gill samples

2010
Miscellaneous
Crassostrea gigas
DNazol
Pacific oyster
R51
RNAlater
Set up gDNA isolation from the following samples:
May 27, 2010
Sam White
 

SOLiD ePCR/Templated Bead Prep - Lake Trout Lean library

2010
Miscellaneous
ePCR was performed following ABI’s “full scale” protocol, using 1pM of SOLiD cDNA library.
May 26, 2010
Sam White
 

SOLiD Templated Bead Prep - Yellow perch CT, WB and lake trout Lean libraries (continued from yesterday)

2010
Miscellaneous
Templated bead preparation was performed according to the “full scale” protocol.
May 13, 2010
Sam White
 

SOLiD ePCRs - Yellow perch CT, WB and lake trout Lean libraries

2010
Miscellaneous
Performed ePCRs on these samples from DATE, following the “full scale” protocol. A work flow analysis (WFA) run on these samples from the initial ePCRs/templated bead prep…
May 12, 2010
Sam White
 

Package - Hard Clam gill tissue/hemolymph in RNA later

2010
Miscellaneous
Rec’d package from Rutgers (Emily Pearson) containing two large Ziplock bags on “wet” ice, each of those containing smaller bags with sample tubes in them. One large bag…
May 5, 2010
Sam White
 

DNA Isolation - Qiagen Kit Comparison

2010
Miscellaneous
DNeasy
gDNA
gel
Hyperladder I
troubleshooting
Note: This information was added 20140407. Yes, you read that correctly.
May 5, 2010
Sam White
 

qPCR - V.tubiashii primers test (Vpt A and Vt IGS)

2010
Miscellaneous
Utilized to sets of primers obtained from the Friedman Lab: VptA (referred to as “Hasegawa”, even though the reference article calls the primers Vtp A) and Vt IGS (referred…
May 3, 2010
Sam White
 

Templated Bead Prep SOLiD Libraries - Yellow perch WB, lake trout Lean and Sisco, and herring G/O HWS09 libraries

2010
Miscellaneous
All libraries were prepped according to ABI’s “full-scale” bead prep protocol. Initial bead counts were performed using a hemocytometer in a 1:200 dilution:
Apr 16, 2010
Sam White
 

ePCR SOLiD Libraries - Lake Trout Sisco and Herring G/O HPWS09 libraries (from 20100408)

2010
Miscellaneous
ePCR was performed for the above three mentioned SOLiD libraries using 1.5pM (180 pg/uL) of cDNA, according to the ABI “full scale” ePCR protocol. ePCRs were stored @ 4C…
Apr 15, 2010
Sam White
 

Templated Bead Prep SOLiD Libraries - Abalone CC, CE pools and yellow perch CT, PQ libraries

2010
Miscellaneous
All libraries were prepped according to ABI’s “full-scale” bead prep protocol. Initial bead counts were performed using a hemocytometer in a 1:200 dilution:
Apr 14, 2010
Sam White
 

ePCR SOLiD Libraries - Yellow perch PQ, WB and Lake Trout Lean libraries (from 20100408)

2010
Miscellaneous
ePCR was performed for the above three mentioned SOLiD libraries using 1.5pM (180 pg/uL) of cDNA, according to the ABI “full scale” ePCR protocol. ePCRs were stored @ 4C…
Apr 13, 2010
Sam White
 

ePCR SOLiD Libraries - Abalone CC, CE pools and yellow perch CT SOLiD libraries (from 20100408)

2010
Miscellaneous
Emulsion PCR (ePCR) was performed for the above three mentioned SOLiD libraries using 1.5pM (180 pg/uL) of cDNA, according to the ABI “full scale” ePCR protocol. ePCRs were…
Apr 12, 2010
Sam White
 

cDNA clean up & Bioanalyzer for SOLiD Libraries - Abalone, Yellow Perch, Lake Trout, Herring

2010
Miscellaneous
Amplified cDNA was cleaned up using the Invitrogen PureLink Micro Kit, but was done so according to Ambion’s Whole Transcriptome Analysis Kit protocol and then spec’d.
Apr 8, 2010
Sam White
 

Gel Purification & PCR cDNA SOLiD Libraries - Abalone, Yellow Perch, Lake Trout, Herring

2010
Miscellaneous
cDNA was gel purified according to Ambion’s Whole Transcriptome Analysis Kit. The appropriate regions (100 - 200bp) were excised and cut in to 4, 1x5mm pieces. The two…
Apr 7, 2010
Sam White
 

Reverse Transcription SOLiD Libraries - Abalone, Yellow Perch, Lake Trout, Herring

2010
Miscellaneous
Samples were speedvac’d to dryness and resuspended in 3uL of nuclease-free H2O. Samples were then reversed transcribed according to Ambion’s Whole Transcriptome Analysis…
Apr 6, 2010
Sam White
 

Hibridizaton/Ligation SOLiD Libraries - Abalone, Yellow Perch, Lake Trout, Herring

2010
Miscellaneous
All 8 samples were hybridized/ligated according to Ambion’s Whole Transcriptome Analysis Kit using Adaptor A.
Apr 5, 2010
Sam White
 

Bioanalyzer Total, mRNA and post-fragmentation SOLiD Libraries - Abalone pools

2010
Miscellaneous
0.5uL of fragmented mRNA from each library (combined with 0.5uL) was run on Agilent Bioanalyzer 2100 using RNA Pico chips/reagents according to Agilent’s protocol.
Apr 2, 2010
Sam White
 

RNA Precipitation and Fragmentation for SOLiD Libraries - Pooled abalone mRNA (from yesterday)

2010
Miscellaneous
mRNA was precipitated according to Ambion’s MicroPolyA Purist Kit protocol. Added 0.1vols of ammonium acetate, 2.5vols of 100% EtOH and incubated 30mins @ -80C. Samples were…
Apr 1, 2010
Sam White
 

RNA Precipitation & mRNA Isolation for SOLiD Libraries - Pooled abalone total RNA: Carmel control, Carmel exposed

2010
Miscellaneous
RNA of 8 samples from each group was pooled equally from each individual. RNA was precipitated according to Ambion’s MicroPolyA Purist Kit. Used 0.1 volumes of 3M NaAOc…
Mar 31, 2010
Sam White
 

Bioanalyzer for SOLiD Libraries - Fragmented mRNA from Perch, Lake Trout & Herring RNA samples

2010
Miscellaneous
1uL of each sample from 20100325 was run on the Agilent 2100 Bioanalyzer on a RNA Pico 6000 chip to evaluate RNA quantity and fragmentation.
Mar 29, 2010
Sam White
 

SOLiD Library Prep - mRNA (perch, lake trout, herring from 20100318) Fragmentation

2010
Miscellaneous
Fragmented mRNA according to Ambion’s Whole Transcriptome Sequencing Kit. Cleaned up sample using Ribominus Concentration Module (Invitrogen) according to Ambion’s WTS…
Mar 25, 2010
Sam White
 

Bioanalyzer for SOLiD libraries - Total and mRNA from Perch, Lake Trout & Herring RNA samples (CONTINUED from yesterday)

2010
Miscellaneous
Total and mRNA aliquots (~5ng/uL) were run on the Agilent Bioanalyzer Pico RNA chips.
Mar 18, 2010
Sam White
 

mRNA Precipitation for SOLiD - Perch, Lake Trout, & Herring mRNA (CONTINUED from yesterday)

2010
Miscellaneous
mRNA was pelleted and washed according to Ambion’s MicroPolyA Purist Kit. Pellets were resuspended in 8uL nuclease-free H2O and spec’d. 0.5uL was taken from each sample…
Mar 17, 2010
Sam White
 

mRNA Isolation for SOLiD - Perch, Lake Trout, and Herring total RNA

2010
Miscellaneous
Received pooled lean and siscowet RNA from Rick. Samples will be processed immediately for SOLiD fragment libraries. Two 1.5mL snap cap tubes labelled:
Mar 16, 2010
Sam White
 

PCR - Test Lexie's Mercenaria 18s contamination issue

2010
Miscellaneous
Lexie’s PCR with this primer set and a pool of Mercenria cDNA has yielded contamination in all of her waters. Performed two sets of PCR: one with her existing primer working…
Mar 10, 2010
Sam White
 

qPCR - Mac's BB/DH cDNA from 20091223

2010
PROPS
GSTA and DPGN primer sets used. These are duplicates based on initial differences seen between BB and DH expression. qPCR set up and plate layout here.
Jan 15, 2010
Sam White
 

SOLiD Bead Titration - Herring fragmented cDNA libraries: 2LHKOD09, 4LHTOG09, 6LHPWS09

2010
Miscellaneous
Continued with templated bead prep from ePCRs for these libraries. Samples were processed according to the ABI “Templated Bead Preparation Guide” following the “full-scale”…
Jan 14, 2010
Sam White
 

SOLiD ePCRs - Herring cDNA libraries

2010
Miscellaneous
Using 1.5pM of starting template, based on success of the 3LHSITK09 bead prep (see 20100108).
Jan 13, 2010
Sam White
 

SOLiD ePCR - Herring fragmented cDNA library: 2LHKOD09

2010
Miscellaneous
Using 1.5pM of starting template, based on success of the 3LHSITK09 bead prep (see 20100108).
Jan 11, 2010
Sam White
 

qPCRs - Mac's BB/DH cDNA from 20091223

2010
PROPS
GNRR2 and CALL primer sets used. These are duplicates based on initial differences seen between BB and DH expression. qPCR set up and plate layout is here.
Jan 11, 2010
Sam White
 

SOLiD Bead Titration - Herring fragmented cDNA library 3LHSITK09 (CONTINUED from ePCR yesterday)

2010
Miscellaneous
Completed the remainder of the procedure for template bead titration, according to the ABI “Templated Bead Preparation Guide” following the “full-scale” protocol.
Jan 8, 2010
Sam White
 

SOLiD ePCR - Herring fragmented cDNA library: 3LHSITK09

2010
Miscellaneous
Due to low yield of templated beads (12x10^6) from the first run through (see SOLiD Bead Titration below), am repeating using 1.5pM of starting template (as opposed to 0.5pM…
Jan 7, 2010
Sam White
 

SOLiD Bead Titration - Herring fragmented cDNA library 3LHSITK09(CONTINUED from ePCR yesterday)

2010
Miscellaneous
Completed the remainder of the procedure for template bead titration, according to the ABI “Templated Bead Preparation Guide” following the “full-scale” protocol.
Jan 7, 2010
Sam White
 

qPCRs - Tim's Adult Gigas gill cDNA (from 20091009)

2010
Miscellaneous
Duplicates of earlier qPCRs.
Jan 6, 2010
Sam White
 

SOLiD ePCR - Herring fragmented cDNA library: 3LHSITK09 (from 20091209)

2010
Miscellaneous
Processed herring fragmented cDNA library 3LHSITK09 (88.ng/uL) according to the ABI “Templated Bead Preparation Guide” following the “full-scale” protocol. Made a 1:1000…
Jan 6, 2010
Sam White
 

qPCRs - Tim's Adult Gigas gill cDNA (from 20091009)

2010
Miscellaneous
Duplicates of earlier qPCRs.
Jan 5, 2010
Sam White
 

qPCR - BB & DH cDNA (from 20091223)

2009
PROPS
qPCR was set up on these cDNAs using the following primers:
Dec 31, 2009
Sam White
 

qPCRs - BB & DH cDNA (from 20091223)

2009
PROPS
qPCR was set up on these cDNAs using the following primers:
Dec 30, 2009
Sam White
 

qPCR - BB & DH cDNA (from 20091223)

2009
PROPS
qPCR was set up on these cDNAs using the following primers:
Dec 29, 2009
Sam White
 

Alaska sockeye salmon sampling (with Seebs): Family #13

2009
Miscellaneous
Juvenile sockeye salmon were subjected to initial heat stress of 18C. 10 fish were weighed, measured and then snap frozen in LN2. Samples were transferred to a freezer box…
Dec 29, 2009
Sam White
 

qPCR - BB & DH cDNA (from 20091223) and Emma primer sets for testing

2009
PROPS
qPCR was set up on these cDNAs using the following primers:
Dec 29, 2009
Sam White
 

qPCRs - BB & DH cDNA (from 20091223)

2009
PROPS
qPCR was set up on these cDNAs using the following primers:
Dec 28, 2009
Sam White
 

qPCRs - BB & DH cDNA (from yesterday)

2009
PROPS
qPCR was set up on these cDNAs using the following primers:
Dec 24, 2009
Sam White
 

Sequencing - Mac methylation samples, Sam rhodopsin samples, Lisa samples

2009
Miscellaneous
Samples were submitted for sequencing. Mac prepped all Roberts Lab samples excluding the Opsin VMC gel slice 2 from 20091217-02. The gel slice was purified with Millipore…
Dec 23, 2009
Sam White
 

qPCR - BB & DH cDNA (from earlier today)

2009
PROPS
qPCR was set up on these cDNAs using HMGP_5’/3’ and SPI_5’/3’ primers. qPCR set up and plate layout can be found here.
Dec 23, 2009
Sam White
 

Reverse Transcription - BB & DH DNased RNA (from 20090514)

2009
PROPS
Made a fresh, double batch (50uL rxn instead of 25uL) of cDNA according to Promega MMLV protocol using oligo dT primers. cDNA was put into a plate for faster qPCR loading. cD…
Dec 23, 2009
Sam White
 

PCR - Sepia cDNA

2009
Miscellaneous
This is an exact repeat of the PCR from yesterday, due to inconsistencies between repeated PCRs from yesterday and earlier today. Here’s yesterday’s workup
Dec 17, 2009
Sam White
 

PCR - Sepia cDNA

2009
Miscellaneous
This is an exact repeat of the PCR from yesterday, due to inconsistencies between repeated PCRs from yesterday and earlier today. Here’s yesterday’s workup. Samples were…
Dec 16, 2009
Sam White
 

PCR - Sepia cDNA and DNased RNA

2009
Miscellaneous
Set up PCR on recent Sepia cDNA and DNased RNA samples using both S. officianalis_rhodopsin_F, R primers & Sep_op_F2, R2 primers. After yesterday’s intirguing PCR results…
Dec 16, 2009
Sam White
 

PCR - Sepia cDNA (from yesterday)

2009
Miscellaneous
Set up PCR on recent Sepia cDNA samples using both S. officianalis_rhodopsin_F, R primers & Sep_op_F2, R2 primers. PCR set up is here. Looking back at my old paper (gasp!)…
Dec 15, 2009
Sam White
 

Reverse Transcription - Abalone 07:12 DNased RNA (from 20090623)

2009
Miscellaneous
Spec - DNased Abalone 07:12 RNA
Dec 15, 2009
Sam White
 

Reverse Transcription - Sepia DNased RNA

2009
Miscellaneous
DNase Treatment - Sepia RNA (from 20091204)
Dec 14, 2009
Sam White
 

Bioanalyzer - Herring Liver cDNA for SOLiD Libraries

2009
Miscellaneous
Samples were run on the DNA 1000 chip for cDNA smear analysis.
Dec 11, 2009
Sam White
 

Emulsion PCR - Herring Liver cDNA for SOLiD Libraries

2009
Miscellaneous
Emulsion PCR was performed with the two inner gel bands cut out earlier today according to the Ambio WTK protocol. PCR was run for 15 cycles. After the PCR, the samples were…
Dec 9, 2009
Sam White
 

Reverse Transcription - Herring Liver mRNA for SOLiD Libraries

2009
Miscellaneous
Ligation reactions from yesterday were subject to reverse transcription according to protocol. Master mix workup info is here. Samples were incubated @ 42C, 30mins and then…
Dec 9, 2009
Sam White
 

RNA Adapter Hybridization and Ligation - Herring Liver mRNA for SOLiD Libraries

2009
Miscellaneous
RNA from yesterday was speedvac’d to dryness and resuspended in 3uL of nuclease-free H2O. Samples were mixed with Adaptor Mix A and hybridized according to Ambion WTK…
Dec 8, 2009
Sam White
 

RNA Fragmentation - Herring Liver mRNA for SOLiD Libraries

2009
Miscellaneous
Samples from 20091203. 0.5uL was removed from each and transferred to separate tubes and diluted to < 5ng/uL for subsequent Bioanalyzer analysis using the Pico chip. Samples…
Dec 7, 2009
Sam White
 

RNA Isolation - Sepia samples

2009
Miscellaneous
Isolated RNA from 7 sepia samples received 20091125. Samples were removed from RNA Later, blotted and homogenized in 500uL of TriReagent. 500uL of additional TriReagent was…
Dec 4, 2009
Sam White
 

Sequencing - Dungan Isolates, Lake Trout HRM and Emma DD cloning

2009
Miscellaneous
Submitted 1.5 plates for Sanger sequencing. Dungan isolates prepared by me, Lake Trout HRM prepared by Rony and Emma’s differential display cloning samples prepared by her.…
Dec 3, 2009
Sam White
 

mRNA Precipitation - Herring Liver mRNA for SOLiD Libraries (continued from yesterday)

2009
Miscellaneous
Spun samples 16,000g, 30mins, 4C. Discarded supe, quick spun tubes, removed residual supe, washed with 1mL 70% EtOH. Spun samples 16,000g, 15mins, 4C. Discarded supe, quick…
Dec 3, 2009
Sam White
 

Hard Clam Challenge - QPX Strain S-1 (continued from yesterday)

2009
Miscellaneous
All clams appeared to be alive and well. Most had their siphons out when I arrived to start collecting tissues. Clams were shucked after 24hr challenge. Gill and mantle…
Dec 2, 2009
Sam White
 

RNA Precipitation - Herring Liver RNA for SOLiD Libraries (continued from yesterday)

2009
Miscellaneous
Samples were pelleted for 30mins, 16,000g @ 4C. Supe was discarded, samples quick spun, residual supe removed and then washed with 1mL 70% EtOH. Tubes were vortexed until…
Dec 2, 2009
Sam White
 

RNA Precipitation - Herring Liver RNA for SOLiD Libraries

2009
Miscellaneous
50uL of RNA from each of the following were precipitated O/N @ -20C:
Dec 1, 2009
Sam White
 

Hard Clam Challenge - QPX Strain S-1

2009
Miscellaneous
Challenged 2 FL hard clams and 1 BX hard clam with ~100uL of unwashed, 11 day old cultures. 2 FL hard clams and 1 BX hard clam received ~100uL of QPX media, as controls.…
Dec 1, 2009
Sam White
 

MBL Shipment - Hard Clam gill tissue in RNA Later

2009
Miscellaneous
Received samples from Scott Lindell today. Two Ziplock bags taped together labelled “11/16/09 Clams scudders.” The bags contain 2mL screw cap tubes with small tissue samples…
Dec 1, 2009
Sam White
 

MBL Shipment - Sepia tissue samples

2009
Miscellaneous
Received sepia tissue samples in RNA Later from Kendra Buresch. Here’s the list of tissue we received, according to the Post-It with the samples:
Nov 25, 2009
Sam White
 

MBL Shipment - Hard Clams

2009
Miscellaneous
Received hard clams from Scott Lindell today. Two bags. One group (4 live clams, 1 empty shell) labelled as “FL” and another group (9 live clams) labelled as “BX.” Clams…
Nov 24, 2009
Sam White
 

Herring 454 Data

2009
Miscellaneous
Data from MoGene was received today on two DVDs and one HDD. Data is two runs of two libraries, due to MoGene concerns that the data of the first run looked bad (too few…
Nov 19, 2009
Sam White
 

MBL Shipment - MV oysters/cod

2009
Miscellaneous
Received a shipment of various MV oysters/cod samples from Scott Lindell at MBL. However, these were NOT shipped on dry ice! Samples were put @ -80C. Will be organized at a…
Nov 19, 2009
Sam White
 

PCR - "Unknown" Dungans/Lyons

2009
Miscellaneous
This is a repeat of yesterday’s set up with LABY primers, but with an annealing temp of 53C in hopes of improving the number of amplicons generated from additional samples.…
Nov 18, 2009
Sam White
 

PCR - "Unkown" Dungans/Lyons

2009
Miscellaneous
This was done on the numbered tubes using the LABY A/Y primers for eventual sequencing. Turns out many of the tubes have some info (other than just a number) on their sides…
Nov 17, 2009
Sam White
 

Hard Clams - Shipment from Rutgers

2009
Miscellaneous
Received Hard Clam gill samples on “wet ice” in RNA Later from Rutgers. Samples were collected on 11/4/09 (clams held in refrigerator) and preserved (gill tissue collected)…
Nov 13, 2009
Sam White
 

Sequencing - Lake Trout HRM

2009
Miscellaneous
This is a second submission of 12 individuals from 8 primer sets. The previous sequencing run was botched because I used the combined primer plate instead of a single…
Nov 10, 2009
Sam White
 

Oyster CO2/Mechanical Stress - Water quality

2009
Miscellaneous
See Rachel’s 441 Notebook from 10/28/2009 through 11/4/2009 for experiment info. 500mL of water was collected from the CO2 and the air tanks. Water was vacuum filtered…
Nov 5, 2009
Sam White
 

Sample Submissions to MoGene for 454 Analysis - Herring Liver and Testes mRNA

2009
Miscellaneous
Samples Submitted
Submitted 400ng of liver mRNA (SR01) and 400ng of testes (gonad) mRNA (SR02) to MoGene. Samples were packed in dry ice and FedEx.
Oct 27, 2009
Sam White
 

mRNA Isolation - Herring gonad/ovary RNA (from 20091023)

2009
Miscellaneous
Sample was spun 16,000g, 30mins, 4C. Supe removed. Pellet washed with 1mL 70% EtOH. Spun 16,000g, 10mins, 4C. Supe removed. Pellet resuspended in 250uL of nuclease free H2O.…
Oct 27, 2009
Sam White
 

RNA Precipitation - Herring gonad/ovary RNA (from 20091023)

2009
Miscellaneous
A subset (3 samples from each group) of samples were pooled (see spreadsheet, green-highlighted samples), each providing ~7.5ug of RNA, yielding 112.17uL. 0.1 vols of 3M…
Oct 26, 2009
Sam White
 

mRNA Isolation - Herring Liver RNA (from 20091021)

2009
Miscellaneous
Isolated mRNA using Ambion’s MicroPolyA Purist Kit according to protocol. Performed two rounds of isolation to decrease residual rRNA carryover that we frequently see after…
Oct 26, 2009
Sam White
 

RNA Precipitation - Herring Liver Samples

2009
Miscellaneous
A subset of samples (4 samples from each group) were pooled (see spreadsheet, green-highlighted samples), each providing ~68ug of RNA. The pooled sample was split into two…
Oct 23, 2009
Sam White
 

RNA Isolation - Herring Gonad/Ovary Samples

2009
Miscellaneous
RNA was isolated according to protocol. Pellets were resuspended in 50uL of 0.1%DEPC-H2O, heated @ 55C for 5 mins, spec’d and stored @ -80C in the “Herring RNA Box #1”.
Oct 23, 2009
Sam White
 

RNA Isolation - Herring Gonad/Ovary Samples

2009
Miscellaneous
From the Seeb Lab. Homogenized entire gonad/ovary samples in 5mL of TriReagent with the sonicator. In essence, based on the manufacturer’s recommendation, this means the…
Oct 22, 2009
Sam White
 

RNA Isolation - Herring Liver Samples

2009
Miscellaneous
RNA was isolated according to protocol. Pellets were resuspended in 200uL of 0.1%DEPC-H2O, heated @ 55C for 5 mins, spec’d and stored @ -80C in the “Herring RNA Box #1”.
Oct 21, 2009
Sam White
 

RNA Isolation - Herring Liver Samples (LHPWS09 1-6)

2009
Miscellaneous
From Seeb Lab. Homogenized entire liver samples in 5mL of TriReagent with the Tissue Tearers. In essence, based on the manufacturer’s recommendation, this means the ratio of…
Oct 20, 2009
Sam White
 

qPCRs - Tim's adult gigas challenge cDNA (from 20091009)

2009
Miscellaneous
Set up qPCR with Cg_P450 primers and TNFRAF3’/5’ primers. Plate layout/setup is here.
Oct 13, 2009
Sam White
 

qPCR - Tim's adult gigas challenge cDNA (from 20091009)

2009
Miscellaneous
Set up qPCR with Cg_HIF1 (hypoxia induced factor 1) primers and prostaglandin E2 primers. Plate layout/setup is here.
Oct 12, 2009
Sam White
 

qPCR - Tim's adult gigas challenge cDNA (from today)

2009
Miscellaneous
Set up qPCR with EF1 primers and IL17 Internal primers. Plate layout/setup is here. Note: gDNA sample used as a “positive” control will NOT amplify with the EF1 primers.
Oct 9, 2009
Sam White
 

Reverse Transcription - Tim's adult gigas challenge DNased RNA (from 20091008)

2009
Miscellaneous
Performed RT rxns. Setup is here. cDNA was subsequently diluted 1:4 (added 75uL H2O to each well) to properly mirror Tim’s previous qPCRs.
Oct 9, 2009
Sam White
 

qPCR - Tim's adults gigas challenge re-DNased RNA (from today)

2009
Miscellaneous
Performed qPCR using q18s primers on re-DNased RNA (1:100 dilution to match final concentration of template after making cDNA). qPCR set up and plate layout are here.
Oct 9, 2009
Sam White
 

DNase Treatment - Re-DNase of Tim's adult gigas challenge RNA (from yesterday)

2009
Miscellaneous
5 samples from yesterday’s treatment still came up on qPCR, so I will re-DNase those 5 samples. Followed standard protocol in Ambion’s Turbo DNA-free kit.
Oct 9, 2009
Sam White
 

qPCR - Tim's adults gigas challenge DNased RNA (from today)

2009
Miscellaneous
Previous qPCR was done incorrectly (wrong primers), so am repeating with the correct primers. Performed qPCR using q18s primers on DNased RNA (1:100 dilution to match final…
Oct 8, 2009
Sam White
 

qPCR - Tim's adults gigas challenge DNased RNA (from today)

2009
Miscellaneous
Performed qPCR using q18s primers on DNased RNA (1:100 dilution to match final concentration of template after making cDNA). qPCR set up and plate layout are here.
Oct 8, 2009
Sam White
 

DNase Treatment - Tim's adult gigas challenge RNA (from 20090930)

2009
Miscellaneous
Used 5uL of RNA from each sample, brought samples up to 50uL with H2O and treated according to Ambion’s Turbo DNA-free kit. Rigorous protocol was followed (1.5uL DNase…
Oct 8, 2009
Sam White
 

Bioanalyzer Submission - Trout RBC, Colleen's gigas GE sample, Mac's DH/BB PCR for SOLiD WTK

2009
Miscellaneous
Samples were delivered for analysis on the DNA 1000 chip.
Oct 7, 2009
Sam White
 

Reverse Transcription/cDNA purification/Emulsion PCR - Ligation rxns of trout fragmented RNA for SOLiD WTK (from yesterday)

2009
Miscellaneous
The four samples from yesterday were prepared according to the Agilent SOLiD WTK protocol. Briefly:
Oct 6, 2009
Sam White
 

Adapter Ligation - Rick's trout fragmented control/poly I:C samples for SOLiD WTK

2009
Miscellaneous
See the Next Gen Seq Library Database for more info. Processed the 4 samples (one set Ribominus only, one set Ribominus + PolyA enriched) according to the Agilent WTK.…
Oct 5, 2009
Sam White
 

qPCR - Tim's adults gigas challenge DNased RNA (from 20091002)

2009
Miscellaneous
Performed qPCR using q18s primers on DNased RNA (1:100 dilution to match final concentration of template after making cDNA). qPCR set up and plate layout are here.
Oct 5, 2009
Sam White
 

DNase Treatment - Tim's adult gigas challenge RNA (from 20090930)

2009
Miscellaneous
Used 5uL of RNA from each sample, brought samples up to 50uL with H2O and treated according to Ambion’s Turbo DNA-free kit. Transferred treated samples to a PCR plate to…
Oct 2, 2009
Sam White
 

qPCRs - Check gDNA contamination with EF1 & 18s primers in gigas gill RNA (from yesterday)

2009
Miscellaneous
Ran qPCR on RNA to evaluate gDNA contamination in the samples. Dilutions of the RNA were made at 1:100, which would be the equivalent amount when making cDNA (1:25) and…
Oct 1, 2009
Sam White
 

RNA Isolation - Tim's adult gigas challenge samples

2009
Miscellaneous
RNA was isolated using 500uL of TriReagent for all samples. Samples were resuspended in 100uL of 0.1%DEPC-H2O and spec’d. Samples stored in Tim’s “NAME OF BOX” box.
Sep 30, 2009
Sam White
 

Bioanalyzer Submission - Rick's trout RBC samples (various dates)

2009
Miscellaneous
Submitted Rick’s trout RBC samples to FHRC for bioanalysis using the PicoChip for use with the SOLiD WTK. Submission sheet is here (dead link - linked to 20090929-01.jpg on…
Sep 29, 2009
Sam White
 

RNA Fragmentation - Rick's trout RBC samples prepped earlier today

2009
Miscellaneous
Continued precipitation. Spun samples 30 mins, 16,000g, 4C. Removed supe. Added 1mL 70% EtOH. Spun samples 15mins, 16,000g, 4C. Removed supe. Resuspended in 8uL H2O.…
Sep 29, 2009
Sam White
 

EtOH Precipitation - Rick's trout Ribosomoal-depleted RNA for SOLiD WTK (from today)

2009
Miscellaneous
The “control” and “poly I:C” samples prepared earlier today were EtOH precipitated in preparation for fragmentation.
Sep 28, 2009
Sam White
 

Ribosomal-depleted RNA - Rick's trout RBC samples for the SOLiD WTK

2009
Miscellaneous
Prior to starting the procedure, 0.5uL of total RNA was removed from each sample (control, polyI:C), diluted to ~5ng/uL. 1.5uL of each of these was transferred to a 0.5mL…
Sep 28, 2009
Sam White
 

RNA Fragmentation - Rick's trout RBC samples prepped earlier today (see below)

2009
Miscellaneous
Samples were fragmented according to the Whole Transcriptome Kit protocol. Samples were then cleaned up using Invitrogen’s Modified RiboMinus Concentration Module, according…
Sep 23, 2009
Sam White
 

mRNA Isolation - Rick's trout RBC samples previously treated with Ribominus Kit (by Mac)

2009
Miscellaneous
Was given ~0.5ug of each of these two RNA samples and processed them with Ambion’s microPolyA Purist Kit according to protocol. After elution, the samples were EtOH…
Sep 23, 2009
Sam White
 

mRNA Isolation - Gigas BB and DH samples previously treated with Ribominus Kit (by Mac)

2009
Miscellaneous
Was given ~0.5ug of each of these two RNA samples and processed them with Ambion’s microPolyA Purist Kit according to protocol. After elution, the samples were EtOH…
Sep 18, 2009
Sam White
 

mRNA Isolation - Gigas BB and DH samples previously treated with Ribominus Kit (by Mac)

2009
Miscellaneous
Was given 1ug of each of these two RNA samples and processed them with Promega’s PolyA Tract Kit according to protocol. After elution, the samples were EtOH precipitated @…
Sep 16, 2009
Sam White
 

HRMs - Lake Trout SNPs (HRM_white-05 & HRM_white_06)

2009
Miscellaneous
The following primers from primer plate LTP01 will be used for analysis of Rick’s Lake Trout DNA1 plate (from 4/28/2009): G10, C11, H11, A12. HRM set up is here. It is the…
Sep 15, 2009
Sam White
 

HRMs - Lake Trout SNPs (HRM_white-03 & HRM_white-04)

2009
Miscellaneous
The following primers from primer plate LTP01 will be used for analysis of Rick’s Lake Trout DNA1 plate (from 4/28/2009): E4, B5, A7, D7. HRM set up is here. It is the same…
Sep 10, 2009
Sam White
 

HRM - Lake Trout SNPs (HRM_white-02)

2009
Miscellaneous
The following primers from primer plate LTP01 will be used for analysis of Rick’s Lake Trout DNA plate (from 4/28/2009): A3, D3, G3, A4. HRM set up is here. It is the same…
Sep 9, 2009
Sam White
 

HRM - Lake Trout SNPs (HRM-white-01)

2009
Miscellaneous
The following primers from primer plate LTP01 will be used for analysis of Rick’s Lake Trout DNA plate (from 4/28/2009): A1, C1, H1, B2. So, that’s 4 primer sets x 96 DNA…
Sep 3, 2009
Sam White
 

qPCR - HRM Lake Trout SNP primer test

2009
Miscellaneous
Tested out the plate of Lake Trout primers (LTP01 - forward and reverse combined) for SNP detection. qPCR was performed using Roche 2x HRM M.M. qPCR set up is here. Cycling…
Sep 1, 2009
Sam White
 

Primers - Lake Trout Primers for HRM

2009
Miscellaneous
The two primer plates (LTP01F, LTP01R) were received today. Primers (supplied as 10 nmoles of each) will be reconstituted with 100uL of PCR H2O to make a Cf of 100uM.…
Aug 27, 2009
Sam White
 

qPCR - Gigas gDNA test of recalibrated Opticon 2

2009
Miscellaneous
Master mix containing Gigas gDNA will be used to verify that the recalibration did work. qPCR setup/plate layout is here. I’ve made a master mix using Cg_HSP70_F/R primers…
Aug 27, 2009
Sam White
 

qPCR - Recalibration of Opticon 2

2009
Miscellaneous
According to the Bio-Rad rep that analyzed the calibration test on 20090824, recalibration might be a good idea. As such, we’ll do that. Old calibration file was found and…
Aug 26, 2009
Sam White
 

DNA Precipitation - C.pugetti DNA for JGI submission (continued from yesterday)

2009
Miscellaneous
Sample was removed from -20C and spun @ 4C, 16,000 x g for 30mins. Supe removed, pellet washed with 1mL 70% EtOH and spun @ 4C, 16,000 x g for 15mins. Supe removed, tube…
Aug 26, 2009
Sam White
 

DNA Precipitation - C.pugetti DNA for JGI submission

2009
Miscellaneous
Precipitate DNA from 20090526 to concentrate and run on gel for resubmission to JGI to see what happens. Added 0.1 volume of 3M sodium acetate, pH = 5.2 (40uL) and 2 volumes…
Aug 25, 2009
Sam White
 

qPCR - Additional Calibration test of Opticon 2

2009
Miscellaneous
Based on recs from Bio-Rad rep (Carl Fisher), will repeat Opticon 2 calibration (see 20090813) test according to Opticon manual. Then, will rotate plate 180 degrees and…
Aug 24, 2009
Sam White
 

qPCR - Carita Primer Test for High Resolution Melt (HRM) Curve Analysis

2009
Miscellaneous
Ran a qPCR on Rick’s Lake Trout DNA from 4/28/2009 using primers in Carita’s CMA01 Primer Plate (Excel file). DNA was pooled (2uL from each sample), spec’d and diluted to…
Aug 17, 2009
Sam White
 

qPCR - Calibration test of Opticon 2

2009
Miscellaneous
Received new FAM calibration reagent. It comes pre-prepared in a 1x PCR buffer (0.3uM), however there is only enough for a single plate (use 50uL/well). Will run plate in…
Aug 13, 2009
Sam White
 

qPCR - Calibration test of Opticon 2

2009
Miscellaneous
Due to results of Opticon testing from 20090722, we have acquired FAM Calibartion Dye from Bio-Rad. Although not listed online or on the product itself, Bio-Rad customer…
Aug 6, 2009
Sam White
 

Bacteria - C.pugetti culture (from 20090713)

2009
Miscellaneous
1L liquid culture (grown for 10 days) was split into two UV-sterilized bottles. Cells were pelleted in a Sorvall T21 centrifuge using the bucket rotor for 30mins @ 4200RPM…
Jul 23, 2009
Sam White
 

qPCR - Gigas DNA for Opticon testing

2009
Miscellaneous
Due to some weird anomolies seen during my previous qPCRs with the H.crach RNA/cDNA samples (positive controls produced good fluorescence when tested in Column 1 of the…
Jul 22, 2009
Sam White
 

RT Rxns - H.crach DNased RNA (from 20090623)

2009
Miscellaneous
DNased RNA was used for cDNA rxns. [Workup of the amount of RNA used in each rxn (472ng/uL) is here (Google…
Jul 22, 2009
Sam White
 

NanoDrop - H.crach DNased RNA (from 20090623)

2009
Miscellaneous
Samples were first spec’d , since they had not been since their DNase treatement.
Jul 21, 2009
Sam White
 

qPCR - Abalone cDNA (07:12 set from 3/3/2009 by Lisa) and DNased RNA (from 20090623)

2009
Miscellaneous
Now that we have a solid positive control, I’ll use the H.crach_h-1fg_intron primers to check the existing cDNA and DNased RNA. qPCR plate layout/set up is here. Anneal temp…
Jul 20, 2009
Sam White
 

qPCR - Abalone gDNA (H.crach 06:7-1)

2009
Miscellaneous
This is to test (again!) the H.crach_h-1fg_intron primers and obtain a working positive control. This gDNA is from Lisa/Nate. Acquired from them 20090717. Don’t know…
Jul 17, 2009
Sam White
 

qPCR - Abalone cDNA (07:12 set from 3/3/2009 by Lisa) and DNased RNA (from 20090623)

2009
Miscellaneous
This is nearly a repeat of the qPCR earlier today due to the fact that the positive control never amplified. This is being done to check whether or not there is gDNA…
Jul 16, 2009
Sam White
 

qPCR - Abalone cDNA (07:12 set from 3/3/2009 by Lisa) and DNased RNA (from 20090623)

2009
Miscellaneous
This is being done to check whether or not there is gDNA contamination in these cDNA and DNased RNA. Will use H.crach_h-1fg_intron primers. gDNA 07:12-15 was used as a…
Jul 16, 2009
Sam White
 

qPCR - Abalone gDNA

2009
Miscellaneous
Used up the remainder of the one positive control gDNA that worked with all the primers in yesterday’s reaction (H.crach_h-1fg_intron, H.iris_actin_intron, H.crach_16s), so…
Jul 15, 2009
Sam White
 

qPCR - Abalone RNA/DNased RNA & "dirty" and "clean" cDNA

2009
Miscellaneous
This was done to really test the detection methods we’re using for gDNA contamination in our qPCRs. qPCR plate layout/set up is here. Anneal temp 50C.
Jul 14, 2009
Sam White
 

PCR - Dungan isolate (MIE-14v) gDNA from 20090708

2009
Miscellaneous
PCR of MIE-14v just to make sure that we can’t get a product from this sample, despite NanoDrop readings suggesting that there’s no DNA. Used both LABY and Euk primer sets. P…
Jul 13, 2009
Sam White
 

Bacteria - C.pugetti large culture

2009
Miscellaneous
One of the three starter liquid cultures from 20090706 wee used to inoculate 1L of Marine Broth + biphenyl. Incubated 200RPM @ 28C.
Jul 13, 2009
Sam White
 

qPCR - Abalone gDNA/cDNA

2009
Miscellaneous
Due to lack of amplification in gDNA samples from 20090710 and 20090708 with either set of intron primers, will repeat with additional gDNA samples to make sure the primers…
Jul 11, 2009
Sam White
 

qPCR - DNased Abalone Dg RNA from 20090625

2009
Miscellaneous
Ran qPCR on gDNA (06:50-10) to test new primers (H.iris_actin_intron_Fw/Rv) designed to bind only to a region in an intron of the H.iris actin gene. Hopefully there’s enough…
Jul 10, 2009
Sam White
 

DNA Precipitation CONTINUED - Dungan MIE-14v gDNA from yesterday

2009
Miscellaneous
Sample was pelleted by spinning in a microcentrifuge @ max speed, 4C for 30mins. Supe was removed and sample CAREFULLY washed with 1mL 70% EtOH. Sample was spun in a…
Jul 9, 2009
Sam White
 

PCR - Bay/Sea Scallop DNA

2009
Miscellaneous
An additional attempt to get the actin primers to work for use in screening samples for bay/sea scallop hybrids. The scallop_actin_fw primer was used in conjunction with the…
Jul 9, 2009
Sam White
 

qPCR - DNased Abalone Dg RNA from 20090625

2009
Miscellaneous
Ran qPCR on DNased Abalone Dg RNA (07:12 Set), gDNA (06:50-10) and clean cDNA (from 20090422) using primers (H.crach_h-1fg_intron_Fw/Rv) designed to bind only to a region in…
Jul 8, 2009
Sam White
 

DNA Precipitation - Dungan MIE-14v gDNA from earlier today

2009
Miscellaneous
Added 1/10 volume of 3M NaOAc (pH = 5.2) to sample (10uL) and then 2 volumes of ice cold 100% EtOH to samples (220uL). Mixed thoroughly and incubated O/N @ -20c.
Jul 7, 2009
Sam White
 

gDNA Isolation - Dungan isolate MIE-14v

2009
Miscellaneous
Cells stored in EtOH were pelleted 5000g, 10mins, 25C. A brownish smear was present along the inside of the tube after spinning; not really a pellet per se. Supe was removed…
Jul 7, 2009
Sam White
 

qPCR - MV hemocyte cDNA from 20090614

2009
Miscellaneous
Set up qPCR with Cv_18s_F/R primers on the following samples that had previously come up negative in both reps using the diluted (1:20) cDNA that Mac had made specifically…
Jul 7, 2009
Sam White
 

Spec Reading - C.pugetti gDNA from 20090526

2009
Miscellaneous
A recent email from JGI indicates that they are satisfied with the quality of DNA (as seen on 20090601), however their estimate of the gDNA concentration (42ng/uL) means…
Jul 6, 2009
Sam White
 

qPCR - MV hemocyte cDNA from 20090614

2009
Miscellaneous
Set up qPCR with Cv_18s_F/R primers on the following samples that had previously come up negative in both reps using the diluted (1:20) cDNA that Mac had made specifically…
Jul 6, 2009
Sam White
 

Bacteria - C. pugetti liquid cultures

2009
Miscellaneous
Inoculated 3 x 5mL Marine Broth + biphenyl crystals (UV sterilized) cultures from frozen stock in 50mL Falcon tubes. Incubated 200RPM, 28C. Will use these are starter…
Jul 6, 2009
Sam White
 

qPCR - MV hemocyte cDNA from 20090614

2009
Miscellaneous
Set up qPCR with Cv_CIAPIN_F/R primers. This is a second rep. Plate layout/PCR set up is here.
Jul 2, 2009
Sam White
 

qPCR - MV hemocyte cDNA from 20090614

2009
Miscellaneous
Set up qPCR with Cv_CatY_F/R primers. This is a second rep. Plate layout/PCR set up is here.
Jul 1, 2009
Sam White
 

qPCR - MV hemocyte cDNA from 20090614

2009
Miscellaneous
Set up qPCR with Cv_CatL_F/R primers. This is a second rep. Plate layout/PCR set up is here.
Jul 1, 2009
Sam White
 

qPCR - MV hemocyte cDNA from 20090614

2009
Miscellaneous
Set up qPCR with Cv_TLR_“short”_F/R primers. This is a second rep. Plate layout/PCR set up is here.
Jul 1, 2009
Sam White
 

qPCRs - MV hemocyte cDNA from 20090614

2009
Miscellaneous
Set up qPCR with Cv_BgBL_F/R primers. This is a second rep. Plate layout/PCR set up is here.
Jun 30, 2009
Sam White
 

qPCRs - MV hemocyte cDNA from 20090614

2009
Miscellaneous
Set up qPCR with Cv_CysB_F/R. Plate layout/PCR set up is here.
Jun 29, 2009
Sam White
 

qPCR - MV hemocyte cDNA from 20090614

2009
Miscellaneous
Set up qPCR with Cv_18s_F/R primers. Plate layout/PCR set up is here. This is a second rep. Used 1:20 cDNA plate made by Mac as template.
Jun 26, 2009
Sam White
 

qPCR - Abalone Dg DNased RNA from yesterday and earlier today

2009
Miscellaneous
Check Abalone RNA for residual gDNA contamination after DNase treatment. Ran qPCR with H.crach_16s_SYB_F/R primers. Plate layout/PCR set up here.
Jun 25, 2009
Sam White
 

DNase Treatment - Abalone Dg RNA

2009
Miscellaneous
DNase treated Abalone Dg RNA. Followed Ambion’s Turbo DNA-free Kit rigorous protocol. Here are the calcs/workup for the DNase treatment. This used previously untreated RNA.
Jun 25, 2009
Sam White
 

qPCRs - MV hemocyte cDNA from 20090614

2009
Miscellaneous
Set up qPCR with Cv_CIAPIN_F/R primers. Plate layout/PCR set up is here.
Jun 24, 2009
Sam White
 

DNase Treatment - Abalone Dg RNA (07:12 set)

2009
Miscellaneous
DNase treated the 07:12 set of Abalone Dg RNA. Also, respec’d the RNA prior to proceeding. Followed Ambion’s Turbo DNA-free Kit rigorous protocol. Here are the calcs/workup…
Jun 24, 2009
Sam White
 

EtOH Precipitation - DNased Abalone Dg RNA from yesterday AND the 07:12 set (DNased by Lisa 20090306)

2009
Miscellaneous
Due to the excessive number of times that these samples have been DNased, I’m concerned that the buffer is becoming too concentrated. So, I’m performing an EtOH precip on…
Jun 23, 2009
Sam White
 

qPCR - MV hemocyte cDNA from 20090614

2009
Miscellaneous
Set up qPCR with Cv_CatL_F/R primers. Plate layout/PCR set up is here.
Jun 22, 2009
Sam White
 

qPCR - DNased Abalone Dg RNA from earlier today AND the 07:12 set (DNased by Lisa 20090306)

2009
Miscellaneous
Set up qPCR using H.crach_16s_SYBR_F/R primers. Plate layout/set up is here.
Jun 22, 2009
Sam White
 

DNase Treatment - Abalone Dg DNased RNA 20090610

2009
Miscellaneous
This is the 4th time this RNA has been DNased. Performed using Ambion’s Tubro DNA-free Kit. Followed the “rigorous” treatment protocol.
Jun 22, 2009
Sam White
 

qPCR - MV hemocyte cDNA from 20090614

2009
Miscellaneous
Set up qPCR with Cv_TLR _short_F/R primers. Plate layout/PCR set up is here.
Jun 18, 2009
Sam White
 

qPCR - MV hemocyte cDNA from 20090614

2009
Miscellaneous
Set up qPCR with Cv_BgBL_F/R primers. Plate layout/PCR set up is here.
Jun 17, 2009
Sam White
 

qPCR - MV hemocyte cDNA: Test Immomix (SYTO13) vs. Strategene SYBR

2009
Miscellaneous
Due to craziness seen in melting curves, fluorescence, and empty wells from the previous run, will compare SYTO vs. SYBR with select MV cDNAs. Additionally, acquired some…
Jun 15, 2009
Sam White
 

qPCR - MV hemocyte cDNA from yesterday

2009
Miscellaneous
qPCR set up/plate layout is here. Used Cv_18s_F/R primers to assess samples’ “useability” for future qPCRs. Used an ABI optically clear adhesive film instead of caps. Ran…
Jun 15, 2009
Sam White
 

Reverse Transcription - MV hemocyte DNased RNA from 20090612

2009
Miscellaneous
Made cDNA using Promega M-MLV RT and oligo dT primers. RT rxn set up is here. Samples were stored @ 4C until ready to use.
Jun 14, 2009
Sam White
 

qPCR - DNased MV hemocyte RNA from earlier today AND Turbo kit test

2009
Miscellaneous
qPCR set up/plate layout is here. Used Cv_18s_F/R primers for the MV hemocyte RNA and Gigas_18s_F/R primers for the Turbo kit test. Anneal 55C.
Jun 12, 2009
Sam White
 

DNase Treatment - MV hemocyte RNA from yesterday

2009
Miscellaneous
Samples 3326: B23, A25, A22, B14, A21, A10 B22 came up positive for gDNA still. These were retreated according to Ambion protocol with a brand new Turbo DNA-free DNase kit.…
Jun 12, 2009
Sam White
 

DNase Treatment - MV hemocyte RNA from earlier today

2009
Miscellaneous
The entire 20uL of RNA were treated with Ambion’s Turbo DNA-free kit according to protocol and spec’d.
Jun 11, 2009
Sam White
 

RNA Isolation - Martha's Vineyard (MV) hemocytes

2009
Miscellaneous
Samples were pelleted at 100g, 4C for 10mins. The supe was mostly removed, leaving ~50uL of supe above the pellets. RNA was isolated according to the TriReagent protocol…
Jun 11, 2009
Sam White
 

qPCR - Re-DNased abalone Dg RNA from earlier today

2009
Miscellaneous
This is a repeat of the previous qPCR from earlier today, BUT I think I might have used the wrong primers in the earlier qPCR (see below). Set up qPCR with the correct (I’m…
Jun 10, 2009
Sam White
 

qPCR - Re-DNased abalone Dg RNA from earlier today

2009
Miscellaneous
Set up qPCR. Plate layout/workup is here.
Jun 10, 2009
Sam White
 

DNase Treatment - Abalone Dg DNased RNA from 20090605

2009
Miscellaneous
This is the 3rd time this will be performed on these samples. Hopefully using a different (i.e. new) kit will work. Not sure what’s going on here. Performed according to…
Jun 10, 2009
Sam White
 

PCR - C.pugetti gDNA from 20090526

2009
Miscellaneous
This is a repeat of yesterday’s PCR due to the presence of bands in the water-only samples. Will use reagents and universal 16s bacterial primers (27F & 1492R) provide by…
Jun 9, 2009
Sam White
 

PCR - C.pugetti gDNA from 20090513 & 20090526

2009
Miscellaneous
Previous PCRs from 20090601 & 20090602 both showed contamination in the negative control. Suspect that the primer stocks were contaminated due to the usage of older…
Jun 8, 2009
Sam White
 

qPCR - Re-DNased abalone Dg RNA from earlier today

2009
Miscellaneous
Done to verify removal of gDNA from RNA. Used H.crach_16s_syb_f/r primers. PCR workup/plate layout is here.
Jun 8, 2009
Sam White
 

DNase Treatment - Abalone Dg DNased RNA from 20090605

2009
Miscellaneous
Had to re-treat these samples due to residual gDNA that was NOT eliminated the first time through. Possible old Ambion kit??
Jun 8, 2009
Sam White
 

Bacteria - C.pugetti culture (1x 1L)

2009
Miscellaneous
Inoculated 1x 1L of MB + biphenyl crystals from frozen stock. Incubated 28C, 200RPM. MB was autoclaved with the biphenyl crystals.
Jun 5, 2009
Sam White
 

qPCR - DNased abalone Dg RNA from earlier today

2009
Miscellaneous
Done to verify removal of gDNA from RNA. Used H.crach_16s_syb_f/r primers. PCR workup/plate layout is here.
Jun 5, 2009
Sam White
 

DNase Treatment - Abalone Dg RNA isolated yesterday and from 20090518

2009
Miscellaneous
RNA from yesterday was treated according to Ambion Turbo DNA-free protocol to remove gDNA contamination. Work up is here.
Jun 5, 2009
Sam White
 

RNA Isolation - Abalone Dg Project Samples

2009
Miscellaneous
RNA was isolated from the following samples using the MoBio RNA PowerSoil Kit according to protocol:
Jun 4, 2009
Sam White
 

DNase Treatment - Abalone Dg RNA isolated yesterday

2009
Miscellaneous
RNA from yesterday was treated according to Ambion Turbo DNA-free protocol to remove gDNA contamination. Work up is here. Will check for residual gDNA contamination once…
Jun 3, 2009
Sam White
 

PCR - C.pugetti DNA from 20090513 & 20090526

2009
Miscellaneous
This is a repeat of yesterday’s PCR with a fresh working stock in hopes of eliminating the source of contamination seen in the negative control yesterday.
Jun 2, 2009
Sam White
 

RNA Isolation - Abalone Dg Project

2009
Miscellaneous
Isolated RNA using the MoBio RNA PowerSoil Kit according to protocol from the following samples:
Jun 2, 2009
Sam White
 

PCR - C.pugetti DNA from 20090513 & 20090526

2009
Miscellaneous
Performed PCR as set up here using universal bacterial 16s primers (sequences provided by Sara Kelly).
Jun 1, 2009
Sam White
 

DNA Gel - JGI QC check of C. pugetti DNA from 20090526

2009
Miscellaneous
Lane 1 - 15ng standard (5uL)
Jun 1, 2009
Sam White
 

gDNA Isolation - C. pugetti (from 20090518)

2009
Miscellaneous
Followed JGI “Bacterial genomic DNA isolation using CTAB” protocol(Word doc) with the following notes/changes.
May 26, 2009
Sam White
 

DNA Methylation Test - Gigas site gDNA (BB & DH) from 20090515

2009
Miscellaneous
Used BB & DH samples #11-17 for procedure. Followed Epigentek’s protocol. My calcs for dilutions/solutions needed are here. All solutions were made fresh before using…
May 19, 2009
Sam White
 

RNA Isolation - Abalone Dg Project samples

2009
Miscellaneous
Isolated RNA from Abalone Dg samples (see below) using MoBio RNA PowerSoil Kit according to protocol. RNA was stored @ -80C.
May 18, 2009
Sam White
 

C.pugetti - Liquid Cultures

2009
Miscellaneous
Inoculated 2 x 1L of 1x Marine Broth + biphenyl crystals (in 2L flasks) using 5mL of liquid culture from 20090501. Incubated at 28C 200RPM.
May 18, 2009
Sam White
 

gDNA Isolation - Gigas Dermo Samples

2009
Miscellaneous
Transferred tissue from previously Chelexed samples:
May 15, 2009
Sam White
 

gDNA Isolation - Mac's BB and DH site samples

2009
PROPS
Due to failure of gDNA isolation via the TriReagent method (see 20090511) used Qiagen DNeasy Kit. Digested samples for 3 hrs. at 55C in Proteinase K according to protocol.…
May 15, 2009
Sam White
 

Reverse Transcription - Mac's gigas DNased RNA from 20090512

2009
PROPS
Performed RT using Promega M-MLV RT according to M-MLV protocol and used 0.5ug oligo dT per ug of RNA on all BB and DH site samples that were negative for gDNA (see qPCR…
May 14, 2009
Sam White
 

gDNA Isolation - C.pugetti

2009
Miscellaneous
Isolated according to JGI protocol (Word doc). Used 100mL, 8 day old culture inoculated from a plate on 20090505. Resuspended pellets in 740uL of TE and took an OD600 via…
May 13, 2009
Sam White
 

qPCR - Mac's gigas DNased RNA from earlier today

2009
PROPS
Performed qPCR on the DNased oyster RNA from earlier today with Gigas_18s_F/R primers to verify removal of detectable gDNA in the samples, since the qPCR from 20090508…
May 12, 2009
Sam White
 

DNase Treatment (Rigorous!) - Mac's gigas RNA/Re-DNased RNA from 20090507 & 20090508, respectively

2009
PROPS
Followed the rigorous protocol for Ambion’s Turbo DNA-free protocol for the following RNAs:
May 12, 2009
Sam White
 

DNA Isolation - Mac's gigas samples from 20090505 & 20090506

2009
PROPS
Isolated gDNA according to Molecular Research Center TriReagent protocol from BB#1-20 and DH#1-20. Resuspended DNA in 600uL of 8mM NaOH. Spec.
May 11, 2009
Sam White
 

qPCR - Re-DNased oyster RNA from today

2009
PROPS
Performed qPCR on the re-DNased oyster RNA from earlier today with Gigas_18s_F/R primers to verify removal of detectable gDNA in the samples, since the initial qPCR from…
May 8, 2009
Sam White
 

DNase Treatment - Oyster RNA from yesterday

2009
PROPS
Yesterday’s qPCR indicated that all of the RNA still contained gDNA contamination. So, took 10ug of RNA from BB #1-10 and DH#1-10 (calcs/workup BB and DH) and brought the…
May 8, 2009
Sam White
 

qPCR - DNased oyster RNA from earlier today

2009
PROPS
Performed qPCR on the DNased RNA to with Gigas_18s_F/R primers to verify removal of detectable gDNA in the samples. Plate layout/set up can be found here.
May 7, 2009
Sam White
 

DNase Treatment - Oyster RNA from today

2009
PROPS
All of the RNA (50uL) was DNase treated with Ambion’s Turbo DNA-free kit according to protocol. Samples were spec’d.
May 7, 2009
Sam White
 

RNA Isolation - Mac's oyster tissues (BB and DH) (CONTINUED from yesterday)

2009
PROPS
Samples were precipitated according to TriReaget protocol. RNA was resuspended in 50uL of 0.1% DEPC-H2O and then heated @ 55C for 10mins to help dissolve the pellets.…
May 7, 2009
Sam White
 

RNA Isolation - Mac's oyster tissues (BB and DH) (CONTINUED from yesterday)

2009
PROPS
Completed the reaminder of the samples (BB#9-20 and DH#1-20) up to the point of precipitation. Isopropanol was added and stored @ -20C. Organic phase was retained for…
May 6, 2009
Sam White
 

Bacteria - C. pugetti liquid cultures

2009
Miscellaneous
Started two 100mL cultures in 1x Marine Broth + biphenyl. One culture was inoculated from the original liquid culture (from 20090419) and the second was inoculated with a…
May 5, 2009
Sam White
 

RNA Isolation - Mac's oyster tissues (BB and DH)

2009
PROPS
Processed BB#1-8 up to the point of precipitation. Added isopropanol and stored @ -20C. Organic phase was retained for subsequent gDNA isolation and stored @ 4C.
May 5, 2009
Sam White
 

Bacteria - C. pugetti liquid cultures

2009
Miscellaneous
Inoculated a total of 10, 5mL 1x Marine Broth in 50mL conicals. 5 tubes received 1mL of the original culture started on 20090419. 4 tubes received 1mL of the secondary…
May 1, 2009
Sam White
 

Bacteria - C. pugetti plate (from 20090424)

2009
Miscellaneous
An additional yellowing has occurred on the plate. This is in accordance with the Dyksterhouse et al. paper. Colonies still barely visible.
Apr 30, 2009
Sam White
 

Bacteria - C. pugetti plate (from 20090424)

2009
Miscellaneous
There appears to be growth on the plate. There is a large, bright yellow/chartreuse region on the plate where the streaking was initiated. Additionally, upon close…
Apr 29, 2009
Sam White
 

Bacteria - C. pugetti liquid culture

2009
Miscellaneous
Results: It has now been 8 days since revival of the ATCC freeze dried culture. The media still looks a bit cloudy, but hasn’t really changed since the second or third day…
Apr 27, 2009
Sam White
 

Bacteria - C. pugetti plate

2009
Miscellaneous
Streaked C. pugetti onto marine broth plate + a few biphenyl crystals and incubated at RT over the weekend.
Apr 24, 2009
Sam White
 

Reverse Transcription - cDNA from DNased Abalone RNA from 20090420

2009
Miscellaneous
black abalone
DNased RNA
Haliotis cracherodii
M-MLV
reverse transcription
RNA
Prepared cDNA using an equal amount of RNA from all samples (442.6ng)(https://spreadsheets.google.com/ccc?key=0AmS_90rPaQMzcHdyU1d0MDVMLWphMFdTOHUwVHFqWnc&hl=en). This…
Apr 22, 2009
Sam White
 

qPCR - Abalone DNased RNA from yesterday

2009
Miscellaneous
Performed qPCR to evaluate gDNA removal w/ 2x Immomx and SYTO 13. qPCR/plate set up is here.
Apr 21, 2009
Sam White
 

Bacteria - C. pugettii culture CONTINUED (from 20090419)

2009
Miscellaneous
Transferred 1mL of the culture to a 50mL conical containing 4mL of 1x Marine Broth and a couple crystals of biphenyl. Kept the cap loosened and incubated at 20C with shaking…
Apr 21, 2009
Sam White
 

gDNA Removal - Abalone RNA from 20090402 and 20090331

2009
Miscellaneous
Transferred 50uL of RNA to fresh tubes and processed them using the Ambion Turbo DNA-free kit according to the manufacturer’s protocol.
Apr 20, 2009
Sam White
 

Bacteria - C. pugettii culture

2009
Miscellaneous
Rehydrated ATCC isolate according to directions. Added 5mL of 1x Marine Broth to a glass culture tube. Used 1mL of this to rehydrate ATCC sample and then added back into the…
Apr 19, 2009
Sam White
 

Sequencing - Dungan isolates

2009
Miscellaneous
Submitted two plates for sequencing. Each sample two times from each direction.
Apr 17, 2009
Sam White
 

PCR - Two new Dungan isolates

2009
Miscellaneous
Repeat of yesterday’s PCR, but with AmpliTaq, less gDNA and 50uL rxn volume. PCR set up is here.
Apr 16, 2009
Sam White
 

qPCR - Rab7_SYBR primers on abalone RNA and DNased RNA

2009
Miscellaneous
Attempt to find out if gDNA contamination exists iafter Ambion treatment. Previous test (on 20090414) suggests the QT Kit did not eliminate gDNA. PCR set up and plate layout…
Apr 15, 2009
Sam White
 

PCR - Two new Dungan isolates from earlier today

2009
Miscellaneous
Set up PCRs on:
Apr 15, 2009
Sam White
 

gDNA Isolation - Two new Dungan isolates

2009
Miscellaneous
Isolated gDNA from the following two samples:
Apr 15, 2009
Sam White
 

PCR - Test QT Kit with No RT Abalone rxns from 20090408

2009
Miscellaneous
Anneal 55C. [PCR set up is here (bottom half of sheet)(https://eagle.fish.washington.edu/Arabidopsis/Notebook%20Workup%20Files/20090414-01.jpg).
Apr 14, 2009
Sam White
 

PCR - Bay/Sea scallop gDNAs

2009
Miscellaneous
Used higher annealing temps to improve primer specificity, compared to yesterday’s results. PCR set up and plate layout is here.
Apr 14, 2009
Sam White
 

PCR - Bay/Sea scallop gDNA isolated earlier today

2009
Miscellaneous
Used 3 sets of reverse primers:
Apr 13, 2009
Sam White
 

gDNA Isolation - Bay/Sea Scallop and hybrid samples

2009
Miscellaneous
gDNA was isolated using 500uL of 10% Chelex. Samples were heated @ 95C for 1hr w/periodic vortexing. Samples were then spun 16,000g for 5mins @ 4C. Stored @ -20C in Bay x…
Apr 13, 2009
Sam White
 

PCR - Abalone gDNA/RNA/cDNA w/new TOLLIP primer

2009
Miscellaneous
Performed a new PCR on the three types of samples listed above with new TOLLIP primers. The new TOLLIP primers (H.discus_806_F/Ab_866_Rv) surround a putative intron. Thus…
Apr 10, 2009
Sam White
 

PCR - Old Dungan isolates #1-35 w/EukA/B primers

2009
Miscellaneous
Steven had me re-PCR the old Dungan isolates with the new EukA/B primers. Anneal temp 50C. [PCR set up here (bottom half of…
Apr 10, 2009
Sam White
 

PCR - Bay/Sea scallop hybrids

2009
Miscellaneous
Because Rony’s results from her PCR did not match her previous results for the positive controls, I ran the PCRs myself on the controls and the hybrids. Anneal temp 50C. PCR…
Apr 10, 2009
Sam White
 

PCR - Dungan isolates from 20090402 with Euk primers

2009
Miscellaneous
Did PCR with new Euk primers designed by Steven. Should be one step higher taxonomically. PCR set up is here. Aneal temp 50C.
Apr 9, 2009
Sam White
 

qPCR - Check DNased abalone RNA (by Lisa) for gDNA

2009
Miscellaneous
qPCR was performed with 16s_sybr primers on the DNased RNA that Lisa did. Annel temp 55C. Sample set up and plate layout is here.
Apr 9, 2009
Sam White
 

qPCR - Repeat (modified) of yesterday's abalone cDNA check

2009
Miscellaneous
qPCR was performed with 16s_sybr primers on a subset of the “No RT” cDNA rxns from yesterday at both 55C and 60C. Sample set up and plate layout is here.
Apr 9, 2009
Sam White
 

qPCR - Abalone cDNA (QT) from earlier today

2009
Miscellaneous
qPCR was performed with 16s_sybr primers on a subset of the cDNA rxns and all of the “No RT” rxns from earlier to detect the presence of contaminating gDNA. qPCR was also…
Apr 8, 2009
Sam White
 

cDNA - Abalone RNA from 20090331 & 20090402

2009
Miscellaneous
cDNA was made from the above RNA samples using the Qiagen Quantitect RT Kit. The samples were laid out in a PCR plate. 274.2ng of RNA was used in the rxn for each sample…
Apr 8, 2009
Sam White
 

PCR - New Dungan isolates

2009
Miscellaneous
Repeat of PCR from 20090403, but using AmpliTaq and 50C annealing temp. PCR set up is here.
Apr 6, 2009
Sam White
 

PCR - New Dungan isolates

2009
Miscellaneous
Ran PCR with GoTaq on the new Dungan isolate gDNA from yesterday. PCR set up is here. 53C annealing temp.
Apr 3, 2009
Sam White
 

qPCR - Abalone RNA, check for gDNA

2009
Miscellaneous
Abalone RNA isolated from this week was qPCR’s with 16s primers to determine if gDNA contamination was present. PCR/plate layout is here.
Apr 3, 2009
Sam White
 

gDNA Isolation - New Dungan isolates

2009
Miscellaneous
gDNA was isolated from the following using the Qiagen DNEasy Kit:
Apr 2, 2009
Sam White
 

RNA Isolation - Abalone digestive gland samples

2009
Miscellaneous
Total RNA was isolated from the following abalone digestive gland samples using the RNA Powersoil Kit, according to their protocol:
Apr 2, 2009
Sam White
 

RNA Isolation - Abalone digestive gland samples

2009
Miscellaneous
Total RNA was isolated from the following abalone digestive gland samples using the RNA Powersoil Kit, according to their protocol:
Mar 31, 2009
Sam White
 

RNA Isolation - Abalone digestive gland samples

2009
Miscellaneous
Total RNA was isolated from the following abalone digestive gland samples using the RNA Powersoil Kit, according to their protocol:
Mar 27, 2009
Sam White
 

qPCR - Virginica cDNA (see workup sheet below for more info regarding cDNA)

2009
Miscellaneous
Set up qPCR using the following Virginica primers provided by Mac:
Mar 24, 2009
Sam White
 

mRNA Sample Submission Hard clam gill #1 mRNA from 20090313

2009
Miscellaneous
Submitted four samples (4uL of each) for Agilent Bioanlyzer:
Mar 16, 2009
Sam White
 

mRNA Isolation - hard clam gill #1 continued from yesterday

2009
Miscellaneous
Precipitation was continued from yesterday. Samples were resuspended in 25uL of The RNA Storage Solution (from PolyAPursit Kit) and spec’d. Samples were stored @ -80C in…
Mar 13, 2009
Sam White
 

mRNA Isolation - hard clam gill #1 DNased RNA from today

2009
Miscellaneous
DNased RNA from earlier today was split into four equal parts (175uL = 39.8ug). Three will be used for mRNA isolation and the fourth will remain as total RNA. Three of these…
Mar 12, 2009
Sam White
 

RNA Precipitation - Hard clam gill #1 RNA from 20080819

2009
Miscellaneous
DNAsed RNA using Ambion Turbo DNA-free kit, following the rigorous procedure. Diluted total RNA to 0.2ug/uL (Vf = 720uL). Added 1uL DNase and incubated the tube @ 37C for…
Mar 12, 2009
Sam White
 

qPCR - Repeat of qPCR from earlier today with fresh primer working stocks

2009
Miscellaneous
This is an exact repeat of the qPCR from earlier today, but using a fresh working stock of the Vtub_16s_V3 primers. The plate layout/qPCR workup is here.
Mar 2, 2009
Sam White
 

qPCR - Repeat of 20090227 qPCR with clean water

2009
Miscellaneous
This is an exact repeat of the qPCR from Friday, but using a fresh aliquot of water for preparation. The plate layout/qPCR workup is here.
Mar 2, 2009
Sam White
 

qPCR - New 16s primers for V.tubiashii Control vs. Autoclaved gigas samples (see 20090224)

2009
Miscellaneous
qPCR was performed using SensiMix/SYBR “kit” with DNAsed RNA samples from 20090224. This qPCR used the new V.tub_16s_V3 primers in hopes of getting better amplification;…
Feb 27, 2009
Sam White
 

qPCR - Replicate of V.tubiashii Control vs. Autoclaved gigas samples (see yesterday)

2009
Miscellaneous
This is a repeat of the qPCR from yesterday, but without the 16s and OmpW primer sets due to double peaks in melting curves yesterday. Plate layout/qPCR workup is here.
Feb 25, 2009
Sam White
 

qPCR - V.tubiashii Control vs. Autoclaved gigas samples (see below)

2009
Miscellaneous
qPCR was performed using SensiMix/SYBR “kit” with DNAsed RNA samples and cDNA made earlier today. The plate layout/qPCR workup is here.
Feb 24, 2009
Sam White
 

Reverse Transcription - V.tubiashii DNAsed RNA (from yesterday)

2009
Miscellaneous
Set up the MMLV RT rxns with random primers using ~833ng DNAsed RNA (prepared yesterday) according to the Promega MMLV Product Insert. This procedure is slightly different…
Feb 24, 2009
Sam White
 

RNA Isolation - V.tubiashii samples from autoclaved gigas exposure (from 20081218)

2009
Miscellaneous
RNA was isolated from the Control and V.tub+gigas samples from the 0, 1, & 24hr time points using 1mL TriReagent. No visible pellets. Used 20uL of 0.1%DEPC-H2O to resuspend…
Feb 23, 2009
Sam White
 

Epigenetics Experiment - Gigas treatment

2009
Miscellaneous
Set up two containers with 3L seawater and 4 gigas in each container. The treated sample contained:
Feb 20, 2009
Sam White
 

Sample Submission - V.tubiashii Mass Spec

2009
Miscellaneous
Vibrio samples (2-1 and 2-2) from 20090212 were submitted to the mass spec facility.
Feb 18, 2009
Sam White
 

Trypsin digestion - Vibrio 2D spots CONTINUED (from yesterday)

2009
Miscellaneous
Sample prep was continued from yesterday. SpeedVac’d final, pooled elutions for 1.5hrs. Stored tubes @ -80C. Will submit samples 2-1 and 2-2 for mass spec analysis.
Feb 12, 2009
Sam White
 

Trypsin digestion - Vibrio 2D spots from 20081217

2009
Miscellaneous
Samples were prepared according to Goodlett Lab protocol and incubated O/N on LabQuake.
Feb 11, 2009
Sam White
 

mRNA - Submission for Agilent Bioanalyzer

2009
Miscellaneous
Submitted 4uL (108ng/uL) of mRNA from gigas gill (from DATE!; sometime in late August) to the Center for Array Technologies (CART) at UW. Sample was labelled “SR01”.
Feb 6, 2009
Sam White
 

mRNA - Precipitation continued from yesterday

2009
Miscellaneous
Samples were pelleted and washed with 70% EtOH according to Ambion PolyA Purist protocol. Pellets were resuspended in 10uL of The RNA Storage Solution (included in the…
Jan 23, 2009
Sam White
 

mRNA Isolation - Hard Clam gill and hemo RNA

2009
Miscellaneous
mRNA was isolated according to Ambion PolyA Purist protocol. After mixing samples with resin, samples were incubated @ RT for 1hr. Samples were washed per the protocol.…
Jan 22, 2009
Sam White
 

RNA - Hard clam hemo RNA (from 20090121)

2009
Miscellaneous
Hard clam
hemocyte
Mercenaria mercenaria
mRNA
mRNA enrichment
The two RNA samples from yesterday were precipitated and washed according to the Ambion PolyA Purist protocol and resuspended in 50uL of 0.1% DEPC-H2O.
Jan 22, 2009
Sam White
 

RNA Isolation - Hard clam hemo (from 20090121)

2009
Miscellaneous
The 8 hemo samples were pooled and the 4 gonad/d.g. samples were pooled. RNA was isolated. The homo sample was resuspended in 100uL of 0.1%DEPC-H2O and the gonad/d.g. sample…
Jan 21, 2009
Sam White
 

Bleeding/Tissue Collection - Hard Clams

2009
Miscellaneous
Hemos were collected from the remaining 12 clams as before and stored @ -80C. NOTE: 4 hemocyte samples were extremely cloudy. Possibly not hemos? Maybe gonad/d.g.? Gill…
Jan 20, 2009
Sam White
 

RNA - Precipitation of Hard Clam Hemo RNA from 20090116

2009
Miscellaneous
RNA isolated on 20090116 was precipitated over the weekend @ -20C. Samples were treated according to Ambion PolyA Purist protocol and resuspended in 100uL of 0.1% DEPC-H2O.…
Jan 20, 2009
Sam White
 

RNA Isolation - Hard clam gill, hemos

2009
Miscellaneous
RNA was isolated from hard clam gill (0.08g; from 20090109) and from hard clam hemos (from 20090114). One “unknown” sample (from 20090114) was also processed. Pellets were…
Jan 16, 2009
Sam White
 

Bleeding - Hard Clams

2009
Miscellaneous
Bled 7 clams from 20090108 and 20090109. Bled clams using a 23g 1.5 needle on a 3mL syringe. Fluid was gathered and ranged from ~0.4-1.0mL. Hemolymph was transferred to…
Jan 14, 2009
Sam White
 

RNA - Precipitation continued from yesterday

2009
Miscellaneous
Transferred supe to a fresh tube and added 1mL 70% EtOH to remaining pellet. Spun samples max speed @ 4C 30 mins. Removed supe and washed pellets with 1mL 70% EtOH. Spun max…
Jan 14, 2009
Sam White
 

RNA - Reprecipitation of hard clam RNA from yesterday

2009
Miscellaneous
Because of the relatively large size of the pellets vs. the amount of RNA, I think another round of precipitation would be best to help remove additional residual salt…
Jan 13, 2009
Sam White
 

Bleeding - Hard Clams

2009
Miscellaneous
Bled 8 clams from 20090108 and 20090109, #4, 6, 8, 15, 16, 17, 21, 26. Bled clams using a 23g 1.5 needle on a 3mL syringe. Fluid was gathered and ranged from ~0.4-1.0mL.…
Jan 12, 2009
Sam White
 

RNA Isolation - Hard Clam hemolymph from 20090108, 20090109

2009
Miscellaneous
1mL of TriReagent was used to isolate RNA from 3 combined tubes of hemolymph. This resulted in 10 total RNA preps. Pellets were resuspended in 100uL of 0.1% DEPC-H2O and…
Jan 12, 2009
Sam White
 

Bleeding - Hard Clams

2009
Miscellaneous
Bled 24 hard clams using a 23g 1.5 needle on a 3mL syringe. Fluid was gathered and ranged from ~0.4-1.0mL. Hemolymph was transferred to individual 1.5mL snap cap tubes and…
Jan 9, 2009
Sam White
 

Bleeding - Hard Clams

2009
Miscellaneous
Bled 6 hard clams using a 23g 1.5 needle on a 3mL syringe. Fluid was gathered and ranged from ~0.4-1.0mL. Hemolymph was transferred to individual 1.5mL snap cap tubes and…
Jan 8, 2009
Sam White
 

PCR - Dungan Isolates

2009
Miscellaneous
Samples (in Chelex) were vortexed and heated @ 95C for 30mins with periodic vortexing. Tubes were spun max speed @ 4C for 2 mins to pellet Chelex. Set up PCR using Immomix…
Jan 7, 2009
Sam White
 

PCR - Dungan Isolates

2009
Miscellaneous
All samples , except xCVC-11t, are already in Chelex. For xCvC-11t, pipetted a shunk of cells/tissue from source tube. Volume of liquid (EtOH) was ~75uL. Added this to screw…
Jan 6, 2009
Sam White
 

SDS/PAGE, Western Blot - Test of HSP70 Ab on heat stressed shellfish for FISH441

2009
Miscellaneous
Pacific oysters, a mussel, barnacles and a clam (sp. ?) were transferred from the holding tank to a large beaker with sea water which was placed into a 37C water bath. The…
Jan 2, 2009
Sam White
 

SDS/PAGE, Western Blot - Test of new Western Breeze Kit & HSP70 Ab for FISH441

2008
Miscellaneous
anti-HSP70
anti-myc
antibody
Coomassie
Crassostrea gigas
MSTN
MSTN1b
myostatin
Pacific oyster
protein
SDS-PAGE
SeeBlue Plus
Western blot
Western Breeze Chromogenic (anti-mouse) Kit
Ran varying amounts of Gigas Gill 24hr Control protein extract from 20080917 (Notebook link dead - in genefish.wikispaces notebook). See table below:
Dec 31, 2008
Sam White
 

RNA Gel - V. tubiashii mRNA samples (from 20081224)

2008
Miscellaneous
Lane 1 - Empty Lane 2 - Total RNA, Control Lane 3 - mRNA, Control Lane 4 - Total RNA, Vibrio+gigas Lane 5 - mRNA, Vibrio+gigas
Dec 29, 2008
Sam White
 

rRNA Removal - V. tubiashii total RNA from yesterday

2008
Miscellaneous
rRNA removal was continued from O/N precipitation. Processed the samples according to the Ambion MICROBExpress Kit protocol and resuspended final pellets in 25uL of The RNA…
Dec 24, 2008
Sam White
 

RNA Isolation - V. tubiashii from challenge (see 20081216)

2008
Miscellaneous
MICROBExpress Kit
NanoDrop1000
RNA isolation
RNA quantification
TriReagent
Vibrio tubiashii
Added 10mL TriReagent to 2 x 50mL pellets (5.63 x 10^11 total bacteria; see calcs on 20081219 from the control samples collected on 20081219. Added 10mL TriReagent to 1 x…
Dec 22, 2008
Sam White
 

Vibrio challenge CONTINUED (from yesterday)

2008
Miscellaneous
Significantly more bacteria in the container containing autoclaved oysters. Collected 2 x 50mL from each treatment. Collected ~750mL from each treatment. Cells were pelleted…
Dec 19, 2008
Sam White
 

Vibrio challenge CONTINUED (from yesterday)

2008
Miscellaneous
500mL culture was split evenly between two containers containing 3L sterile sea water each. One container also contained 3 large, autoclaved C. gigas. Containers had an air…
Dec 18, 2008
Sam White
 

Vibrio challenge CONTINUED (from yesterday)

2008
Miscellaneous
One of the two starter cultures from yesterday were used to inoculate 500mL 1x LB+1% NaCl and incubated O/N @ 30C 200RPM.
Dec 17, 2008
Sam White
 

Vibrio challenge

2008
Miscellaneous
bacterial challenge
bacterial culture
Vibrio exposure
Vibrio tubiashii
2X 10mL starter cultures of in 1x LB+1% NaCl were inoculated with two separate colonies of V. tubiashii and incubated O/N @ 30C 200RPM.
Dec 16, 2008
Sam White
 

SDS/PAGE/Western - anti-HSP70 Ab Re-test

2008
Miscellaneous
anti-HSP70
antibody
chemiluminescent
Coomassie
Crassostrea gigas
hemocyte
hemolymph
Pacific oyster
protein
SDS-PAGE
SeeBlue Plus
Another attempt to determine appropriate amounts of anti-HSP70 Ab (ABR cat# MA3-006)and/or protein needed for better detection of HSP70 in Gigas protein samples. Gigas gill…
Dec 16, 2008
Sam White
 

SDS/PAGE/Western - Attempt to fix/identify problem(s) with Westerns

2008
Miscellaneous
Will use two different antibodies and two different development methods: chromogenic (Invitrogen Western Breeze) and chemiluminescent.
Dec 12, 2008
Sam White
 

SDS/PAGE/Western - anti-HSP70 Ab test CONTINUED (from yesterday)

2008
Miscellaneous
Primary Ab (anti-HSP70) solution was saved and stored in the 4C. The membrane was washed 3x 10 mins. w/1x TBS-T. 15mL blocking solution was added to membrane and incubated…
Dec 10, 2008
Sam White
 

SDS/PAGE/Western - anti-HSP70 Ab test

2008
Miscellaneous
anti-HSP70
antibody
Coomassie
Crassostrea gigas
gill
mucus
Octopus rubescans
Pacific oyster
protein
red octopus
SDS-PAGE
skin
Test of the new anti-HSP70 Ab (ABR cat# MA3-006). Gigas gill protein extracts from 20080617 (both control and Vibrio exposure samples) were each pooled to result in 10ug…
Dec 9, 2008
Sam White
 

SDS/PAGE/Western - Purified (His column) FST samples from 20081112

2008
Miscellaneous
10uL of each sample from 20081112 (binding supe, washes and elution fractions) were mixed with 2x sample reducing buffer and boiled 5 mins. Samples were loaded onto Pierce…
Nov 17, 2008
Sam White
 

Sequencing - Y2H colony PCRs from 20081112

2008
Myostatin Interacting Proteins
Purified bands were delivered for sequencing. See sequencing log for plate layout/primers.
Nov 14, 2008
Sam White
 

Mass Spec - Band #1 from 20081106

2008
Myostatin Interacting Proteins
Trypsin digested band from MSTN1b + red muscle extract co-IP (~75kDa) was delivered for mass spec analysis. Data in 2-3 weeks.
Nov 14, 2008
Sam White
 

Western Blot - Purified (His column) decorin, FST, LAP & telethonin

2008
Myostatin Interacting Proteins
10uL of each sample from yesterday (binding supe, washes and elution fractions) were mixed with 2x sample reducing buffer and boiled 5 mins. Samples were loaded onto Pierce…
Nov 13, 2008
Sam White
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