University of Washington - SAFS - Roberts Lab

 

Daily Bits - October 2024

2024
Daily Bits
  • In lab.
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 Poly:IC Diploids

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

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

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

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

2022
Miscellaneous
We had some old Crassostrea virginica (Eastern oyster) larval/zygote BS-seq data from the Lotterhos Lab that’s part of the CEABiGR Workshop/Project (GitHub Repo) and Steven…
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

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

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

2022
Computer Servicing
We had been encounterings 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

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

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

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

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…
Jan 31, 2022
Sam White

 

Data Wrangling - C.virginica Gonad RNAseq Transcript Counts Per Gene Per Sample Using 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 (GitHub repo), we decided to compare…
Jan 27, 2022
Sam White

 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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