2023

May 2023

• Trimming and QC - E5 Coral sRNA-seq Trimming Parameter Tests and Comparisons • May 24, 2023
• Data Wrangling - P.meandrina Genome GFF to GTF Using gffread • May 19, 2023
• FastQ QC and Trimming - E5 Coral RNA-seq Data for A.pulchra P.evermanni and P.meandrina Using FastQC fastp and MultiQC on Mox • May 19, 2023
• Data Management - E5 Coral RNA-seq and sRNA-seq Reorganizing and Renaming • May 17, 2023
• Data Received - Coral RNA-seq Data from Azenta Project 30-789513166 • May 16, 2023
• Data Received - Coral sRNA-seq Data from Azenta Project 30-852430235 • May 15, 2023
• lncRNA Expression - P.generosa lncRNA Expression Using StringTie • May 4, 2023
• Daily Bits - May 2023 • May 2, 2023
• lncRNA Identification - P.generosa lncRNAs using CPC2 and bedtools • May 2, 2023

April 2023

• Containers - Apptainer Explorations • April 28, 2023
• Transcript Alignments - P.generosa RNA-seq Alignments for lncRNA Identification Using Hisat2 StingTie and gffcompare on Mox • April 26, 2023
• FastQ Trimming and QC - P.generosa RNA-seq Data from 20220323 on Mox • April 26, 2023
• Data Wrangling - CEABIGR C.virginica Exon Expression Table • April 5, 2023
• Daily Bits - April 2023 • April 3, 2023

March 2023

• Data Wrangling - Append Gene Ontology Aspect to P.generosa Primary Annotation File • March 29, 2023
• Data Received - Trimmed M.magister RNA-seq from NOAA • March 1, 2023

February 2023

• Sequencing Read Taxonomic Classification - P.verrucosa E5 RNA-seq Using DIAMOND BLASTx and MEGAN daa-meganizer on Mox • February 21, 2023
• Data Wrangling - C.goreaui Genome GFF to GTF Using gffread • February 17, 2023
• Transcript Identification and Alignments - P.verrucosa RNA-seq with Pver_genome_assembly_v1.0 Using HiSat2 and Stringtie on Mox • February 16, 2023
• FastQ Trimming and QC - P.verrucosa RNA-seq Data from Danielle Becker in Hollie Putnam Lab Using fastp FastQC and MultiQC on Mox • February 15, 2023
• Data Wrangling - Create P.verrucosa GCA_014529365.1 Karyotype File • February 15, 2023
• Data Received - P.verrucosa RNA-seq and WGBS Full Data from Danielle Becker • February 10, 2023
• Daily Bits - February 2023 • February 1, 2023

January 2023

• Genome Indexing - P.verrucosa v1.0 Assembly with HiSat2 on Mox • January 31, 2023
• Genome Indexing - M.capitata HIv3 Assembly with HiSat2 on Mox • January 31, 2023
• Genome Indexing - P.acuta HIv2 Assembly with HiSat2 on Mox • January 31, 2023
• Data Wrangling - P.verrucosa Genome GFF to GTF Using gffread • January 27, 2023
• Data Wrangling - M.capitata Genome GFF to GTF Using gffread • January 27, 2023
• Data Wrangling - P.acuta Genome GFF to GTF Conversion Using gffread • January 26, 2023
• Genome Indexing - P.verrucosa NCBI GCA_014529365.1 with HiSat2 on Mox • January 25, 2023
• Genome Indexing - M.capitata NCBI GCA_006542545.1 with HiSat2 on Mox • January 25, 2023
• SRA Data - Coral SRA BioProject PRJNA744403 Download and QC • January 13, 2023
• Monthly Goals - January 2023 • January 5, 2023
• Daily Bits - January 2023 • January 3, 2023

2022

</ul>

December 2022

• BS-Seq Analysis - Nextflow EpiDiverse SNP Pipeline for Haws Hawaii C.gigas BAMs from Yaamini Base Config • December 15, 2022
• BS-Seq Analysis - Nextflow EpiDiverse SNP Pipeline for Haws Hawaii C.gigas BAMs from Yaamini • December 14, 2022
• Daily Bits - December 2022 • December 1, 2022

November 2022

• Daily Bits - November 2022 • November 1, 2022

October 2022

• Daily Bits - October 2022 • October 1, 2022

September 2022

• Data Wrangling - C.virginica NCBI GCF_002022765.2 GFF to Gene and Pseudogene Combined BED File • September 26, 2022
• BSseq SNP Analysis - Nextflow EpiDiverse SNP Pipeline for C.virginica CEABIGR BSseq data • September 21, 2022
• Data Wrangling - Identify C.virginica Genes with Different Predominant Isoforms for CEABIGR • September 20, 2022
• RNAseq Alignments - P.generosa Alignments and Alternative Transcript Identification Using Hisat2 and StringTie on Mox • September 14, 2022
• FastQ Trimming - Geoduck RNAseq Data Using fastp on Mox • September 8, 2022
• Daily Bits - September 2022 • September 2, 2022

August 2022

• FastQ Trimming and QC - C.virginica Larval BS-seq Data from Lotterhos Lab and Part of CEABIGR Project Using fastp on Mox • August 29, 2022
• Data Wrangling - Convert S.namaycush NCBI GFF to genes-only BED file for Use in Ballgown Analysis • August 18, 2022
• Splice Site Identification - S.namaycush Liver Parasitized and Non-Parasitized SRA RNAseq Using Hisat2-Stingtie with Genome GCF_016432855.1 • August 10, 2022
• qPCR - Repeat of Mussel Gill Heat Stress cDNA with Ferritin Primers • August 4, 2022
• Daily Bits - August 2022 • August 3, 2022

July 2022

• qPCR - Dorothys Mussel cDNA from 20220726 • July 27, 2022
• RNA Isolation and Quantification - Dorothy Mussel Gill Samples • July 26, 2022
• BS-seq and SNP Analysis - Nextflow EpiDiverse Pipelines Trials and Tribulations • July 25, 2022
• SRA Data - S.namaycush SRA BioProject PRJNA674328 Download and QC • July 6, 2022
• Daily Bits - July 2022 • July 5, 2022

June 2022

• Daily Bits - June 2022 • June 22, 2022
• SRA Submission - Ostrea lurida MBD BS-seq from 20160203 • June 15, 2022

April 2022

• Project Summary - C.virginica CEABiGR - Female vs. Male Gonad Exposed to OA • April 25, 2022
• Data Wrangling - Create Primary P.generosa Genome Annotation File • April 19, 2022
• RNA Isolation - O.nerka Berdahl Brain Tissues • April 11, 2022
• Server Maintenance - Fix Server Certificate Authentication Issues • April 2, 2022

March 2022

• Nextflow - Trials and Tribulations of Installing and Using NF-Core RNAseq • March 25, 2022
• Data Wrangling - P.generosa Genomic Feature FastA Creation • March 24, 2022
• Differential Gene Expression - P.generosa DGE Between Tissues Using Nextlow NF-Core RNAseq Pipeline on Mox • March 23, 2022
• Data Analysis - C.virginica BSseq Unmapped Reads Using MEGAN6 • March 9, 2022
• Data Analysis - C.virginica RNAseq Zymo ZR4059 Analyzed by ZymoResearch • March 2, 2022
• Taxonomic Assignment - C.virginica BSseq Unmapped Reads Using DIAMOND BLASTx and MEGAN6 on Mox • March 2, 2022
• Data Wrangling - P.generosa Genome GFF Conversion to GTF Using gffread • March 1, 2022

February 2022

• Transcript Identification and Alignments - C.virginica RNAseq with NCBI Genome GCF_002022765.2 Using Hisat2 and Stringtie on Mox • February 25, 2022
• Trimming - Additional 20bp from C.virginica Gonad RNAseq with fastp on Mox • February 24, 2022
• Data Wrangling - C.virginica lncRNA Extractions from NCBI GCF_002022765.2 Using GffRead • February 17, 2022
• Transcriptome Assembly - Genome-guided C.virginica Adult Gonad OA RNAseq Using Trinity on Mox • February 7, 2022

January 2022

• RNAseq Alignment - C.virginica Adult OA Gonad Data to GCF_002022765.2 Genome Using HISAT2 on Mox • January 31, 2022
• Data Wrangling - C.virginica Gonad RNAseq Transcript Counts Per Gene Per Sample Using Ballgown • January 27, 2022
• Project Summary - Matt George PSMFC Mytilus Byssus Project • January 13, 2022
• RNA Isolation - O.nerka Berdahl Brain Tissues • January 12, 2022
• RNA Isolation - M.trossulus Gill • January 12, 2022
• RNA Isolation - M.trossulus Gill and Phenol Gland • January 11, 2022
• RNA Isolation - M.trossulus Gill and Phenol Gland • January 10, 2022
• RNA Isolation - M.trossulus Gill and Phenol Gland • January 9, 2022

2021

</ul>

December 2021

• RNA Isolation - M.trossulus Phenol Gland and Gill • December 23, 2021
• RNA Isolation - M.trossulus Foot and Phenol Gland • December 22, 2021
• Project Summary - O.nerka Berdahl Samples • December 22, 2021
• RNA Isolation - O.nerka Berdahl Brain Tissues • December 22, 2021
• RNA Isolation - O.nerka Berdahl Tissues • December 20, 2021
• Data Wrangling - C.virginica NCBI GCF_002022765.2 GFF to Gene BED File • December 9, 2021

October 2021

• Differential Transcript Expression - C.virginica Gonad RNAseq Using Ballgown • October 21, 2021
• SNP Characterization - C.bairdi v3.1 Transcriptome Assembly and Day2 DEG Pooled Samples RNAseq Data • October 5, 2021

September 2021

• SNP Identification - C.bairdi Day 2 DEG Pooled Samples Using bcftools on Mox • September 9, 2021
• RNAseq Alignments - C.bairdi Day 2 Infected-Uninfected Temperature Increase-Decrease RNAseq to cbai_transcriptome_v3.1.fasta with Hisat2 on Mox • September 8, 2021
• Assembly Indexing - C.bairdi Transcriptome cbai_transcriptome_v3.1.fasta with Hisat2 on Mox • September 8, 2021

August 2021

• Computer Servicing - APC SUA2200RM2U UPS Battery Replacement • August 24, 2021
• Computer Management - Disable Sleep and Hibernation on Raven • August 24, 2021
• Uninterruptible Power Supply - Battery Replacement for APS BR1000G • August 11, 2021

July 2021

• Transcript Identification and Quantification - C.virginia RNAseq With NCBI Genome GCF_002022765.2 Using StringTie on Mox • July 26, 2021
• Genome Annotations - Splice Site and Exon Extractions for C.virginica GCF_002022765.2 Genome Using Hisat2 on Mox • July 20, 2021
• Trimming - C.virginica Gonad RNAseq with FastP on Mox • July 14, 2021
• Summary - Geoduck RNAseq Data • July 12, 2021
• Genome Analysis - Identification of Potential Contaminating Sequences in Panopea-generosa-v1.0 Assembly Using BlobToolKit on Mox • July 12, 2021

June 2021

• FastQC-MultiQC - Yaamini's C.virginica RNAseq and WGBS from ZymoResearch on Mox • June 29, 2021
• Data Wrangling - S.salar Gene Annotations from NCBI RefSeq GCF_000233375.1_ICSASG_v2_genomic.gff for Shelly • June 1, 2021

May 2021

• Data Received - Yaamini's C.virginica WGBS and RNAseq Data from ZymoResearch • May 28, 2021
• Assembly Comparisons - Ostrea lurida Non-scaffold Genome Assembly Comparisons Using Quast on Swoose • May 21, 2021
• Assembly Assessment - Olurida_v090 Using Quast on Swoose • May 21, 2021
• Genome Assembly - Olurida_v090 with BGI Illumina and PacBio Hybrid Using Wengan on Mox • May 20, 2021
• Trimming - O.lurida BGI FastQs with FastP on Mox • May 18, 2021
• Genome Submission - Validation of Olurida_v081.fa and Annotated GFFs Prior to Submission to NCBI • May 13, 2021
• RepeatMasker - C.gigas Rosling NCBI Genome GCA_902806645.1 on Mox • May 4, 2021

April 2021

• Singularity - RStudio Server Container on Mox • April 23, 2021
• Read Mapping - 10x-Genomics Trimmed FastQ Mapped to P.generosa v1.0 Assembly Using Minimap2 for BlobToolKit on Mox • April 15, 2021
• Genome Annotation - P.generosa v1.0 Assembly Using DIAMOND BLASTx for BlobToolKit on Mox • April 15, 2021
• Genome Annotation - P.generosa v1.0 Assembly Using BLASTn for BlobToolKit on Mox • April 15, 2021
• Trimming P.generosa 10x Genomics HiC FastQs with fastp on Mox • April 1, 2021

March 2021

• Transcriptome Annotation - Trinotate on C.bairdi Transcriptome v4.0 on Mox • March 18, 2021
• Transcriptome Annotation - DIAMOND BLASTx on C.bairdi Transcriptome v4.0 on Mox • March 18, 2021
• TransDecoder - C.bairdi Transcriptome v4.0 on Mox • March 17, 2021
• Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v4.0 on Mox • March 17, 2021
• Transcriptome Assembly - C.bairdi Transcriptome v4.0 Using Trinity on Mox • March 17, 2021
• Read Extractions - C.bairdi RNAseq Reads from C.opilio BLASTx Matches with seqkit on Mox • March 16, 2021
• DIAMOND BLASTx - C.bairdi RNAseq vs C.opilio Genome Proteins on Mox • March 12, 2021
• Transcriptome Annotation - Trinotate Hematodinium v1.7 on Mox • March 9, 2021
• Transcriptome Annotation - Trinotate Hematodinium v1.6 on Mox • March 9, 2021
• Transcriptome Assembly - Hematodinium Transcriptomes v1.6 and v1.7 with Trinity on Mox • March 8, 2021

February 2021

• Data Wrangling - Gene ID Extraction from P.generosa Genome GFF Using Methylation Machinery Gene IDs • February 26, 2021
• Data Wrangling - Gene ID Extraction from P.generosa Genome GFF Using Methylation Machinery List • February 26, 2021
• SRA Submission - A.elegantissima ONT Fast5 from Jay Dimond • February 9, 2021
• Data Received - Anthopleura elegantissima - aggregating anenome - NanoPore Genome Sequence from Jay Dimond • February 1, 2021

January 2021

• Samples Submitted - M.magister MBD-BSseq Libraries to Univ. of Oregon GC3F • January 12, 2021

2020

</ul>

December 2020

• Transcriptome Comparisons - C.bairdi Transcriptomes Evaluations with DETONATE rsem-eval on Mox • December 29, 2020
• Alignments - C.bairdi RNAseq Transcriptome Alignments Using Bowtie2 on Mox • December 24, 2020
• Samples Received - Cockle Clam Gonad H and E Slides • December 17, 2020
• FastQC-MultiQC - M.magister MBD-BSseq Pool Test MiSeq Run on Mox • December 11, 2020
• Data Received - M.magister MBD-BSseq Pool Test MiSeq Run • December 11, 2020
• Alignment - C.gigas RNAseq to GCF_000297895.1_oyster_v9 Genome Using STAR on Mox • December 8, 2020
• SRA Submission - Haws Lab C.gigas Ploidy pH WGBS • December 7, 2020
• Trimming - Haws Lab C.gigas Ploidy pH WGBS 10bp 5 and 3 Prime Ends Using fastp and MultiQC on Mox • December 6, 2020
• FastQC-MultiQc - C.gigas Ploidy pH WGBS Raw Sequence Data from Haws Lab on Mox • December 6, 2020
• Data Received - C.gigas Diploid-Triploid pH Treatments Ctenidia WGBS from ZymoResearch • December 5, 2020
• Trimming - Ronits C.gigas Ploidy WGBS 10bp 5 and 3 Prime Ends Using fastp and MultiQC on Mox • December 2, 2020
• Sample Submission - M.magister MBD BSseq Libraries for MiSeq at NOAA • December 2, 2020
• Library Quantification - M.magister MBD BSseq Libraries with Qubit • December 2, 2020
• Samples Submitted - Cockle Clam Gonad Histology Cassettes for H and E • December 1, 2020

November 2020

• Trimming - Ronits C.gigas Ploidy WGBS Using fastp and MultiQC on Mox • November 30, 2020
• Bioanalyzer - M.magister MBD BSseq Libraries • November 25, 2020
• MBD BSseq Library Prep - M.magister MBD-selected DNA Using Pico Methyl-Seq Kit • November 24, 2020
• RNA Isolation and Quantification - P.generosa Hemocytes from Shelly • November 19, 2020
• SRA Submission - Ronits C.gigas Ploidy WGBS • November 13, 2020
• FastQC-MultiQc - C.gigas Ploidy WGBS Raw Sequence Data from Ronits Project on Mox • November 10, 2020
• Transcriptome Assessment - Crustacean Transcripome Completeness Evaluation Using BUSCO on Mox • November 10, 2020
• Data Received - C.gigas Ploidy WGBS from Ronits Project via ZymoResearch • November 10, 2020
• Data Wrangling - MultiQC on S.salar RNAseq from fastp and HISAT2 on Mox • November 6, 2020
• Hard Drive Upgrade - Gannet Synology Server • November 5, 2020
• RNAseq Alignments - S.salar HISAT2 BAMs to GCF_000233375.1_ICSASG_v2_genomic.gtf Transcriptome Using StringTie on Mox • November 4, 2020
• RNAseq Alignments - Trimmed S.salar RNAseq to GCF_000233375.1_ICSASG_v2_genomic.fa Using Hisat2 on Mox • November 3, 2020
• MBD Selection - M.magister Sheared Gill gDNA 16 of 24 Samples Set 3 of 3 • November 3, 2020
• MBD Selection - M.magister Sheared Gill gDNA 8 of 24 Samples Set 2 of 3 • November 2, 2020

October 2020

• Trimming - Shelly S.salar RNAseq Using fastp and MultiQC on Mox • October 29, 2020
• MBD Selection - M.magister Sheared Gill gDNA 8 of 24 Samples Set 1 of 3 • October 28, 2020
• DNA Shearing - M.magister gDNA Additional Shearing CH05-01_21 CH07-11 and Bioanalyzer • October 27, 2020
• DNA Shearing - M.magister gDNA Shearing All Samples and Bioanalyzer • October 26, 2020
• DNA Shearing - M.magister CH05-21 gDNA Full Shearing Test and Bioanalyzer • October 22, 2020
• DNA Shearing - M.magister gDNA Shear Testing and Bioanalyzer • October 21, 2020
• 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 • October 14, 2020
• Data Wrangling - C.bairdi NanoPore Reads Extractions With Seqtk on Mephisto • October 13, 2020
• NanoPore Reads Extractions - C.bairdi Taxonomic Reads Extractions with MEGAN6 on 201002558-2729-Q7 and 6129-403-26-Q7 • October 7, 2020
• Comparison - C.bairdi 20102558-2729 vs. 6129-403-26 NanoPore Taxonomic Assignments Using MEGAN6 • October 2, 2020

September 2020

• Taxonomic Assignments - C.bairdi 6129-403-26-Q7 NanoPore Reads Using DIAMOND BLASTx on Mox and MEGAN6 daa2rma on emu • September 28, 2020
• Taxonomic Assignments - C.bairdi 20102558-2729-Q7 NanoPore Reads Using DIAMOND BLASTx on Mox and MEGAN6 daa2rma on emu • September 28, 2020
• Data Wrangling - C.bairdi NanoPore 6129-403-26 Quality Filtering Using NanoFilt on Mox • September 28, 2020
• Data Wrangling - C.bairdi NanoPore 20102558-2729 Quality Filtering Using NanoFilt on Mox • September 28, 2020
• Assembly Assessment - BUSCO C.bairdi Genome v1.01 on Mox • September 24, 2020
• Data Wrangling - Subsetting cbai_genome_v1.0 Assembly with faidx • September 23, 2020
• SRA Submissions - NanoPore C.bairdi 20102558-2729 and 6129_403_26 • September 21, 2020
• Assembly Assessment - BUSCO C.bairdi Genome v1.0 on Mox • September 18, 2020
• Data Wrangling - C.bairdi NanoPore Quality Filtering Using NanoFilt on Mox • September 17, 2020
• Genome Assembly - C.bairdi - cbai_v1.0 - Using All NanoPore Data With Flye on Mox • September 17, 2020
• Taxonomic Assignments - C.bairdi NanoPore Reads Using DIAMOND BLASTx on Mox and MEGAN6 daa2rma on swoose • September 17, 2020
• qPCR - Geoduck Normalizing Gene Primers 28s-v4 and EF1a-v1 Tests • September 16, 2020
• qPCR - Geoduck Normalizing Gene Primer Checks • September 14, 2020
• Data Wrangling - Visualization of C.bairdi NanoPore Sequencing Using NanoPlot on Mox • September 14, 2020
• Data Wrangling - NanoPore Fast5 Conversion to FastQ of C.bairdi 6129_403_26 on Mox with GPU Node • September 4, 2020
• Data Wrangling - NanoPore Fast5 Conversion to FastQ of C.bairdi 20102558-2729 Run-02 on Mox with GPU Node • September 4, 2020
• Data Wrangling - NanoPore Fast5 Conversion to FastQ of C.bairdi 20102558-2729 Run-01 on Mox with GPU Node • September 4, 2020
• Samples Submission - Supplemental Ronits C.gigas Diploid-Triploid Ctendidia gDNA for WGBS by ZymoResearch • September 1, 2020
• DNA Quantification - Re-quant Ronits C.gigas Diploid-Triploid Ctenidia gDNA Submitted to ZymoResearch • September 1, 2020

August 2020

• Transcriptome Annotation - Trinotate C.bairdi v2.1 on Mox • August 31, 2020
• Transcriptome Annotation - Trinotate C.bairdi v3.1 on Mox • August 28, 2020
• Transcriptome Annotation - Trinotate Hematodinium v3.1 on Mox • August 26, 2020
• Transcriptome Annotation - Trinotate Hematodinium v2.1 on Mox • August 26, 2020
• TransDecoder - C.bairdi Transcriptomes v2.1 and v3.1 on Mox • August 26, 2020
• qPCR - P.generosa RPL5 and TIF3s6b v2 and v3 Normalizing Gene Assessment • August 25, 2020
• Sample Submitted - C.gigas Diploid-Triploid pH Treatments Ctenidia to ZymoResearch for WGBS • August 24, 2020
• qPCR - P.generosa RPL5-v2-v3 and TIF3s6b-v2-v3 Primer Tests • August 24, 2020
• DNA Isolation and Quantification - C.gigas High-Low pH Triploid and Diploid Ctenidia • August 21, 2020
• Samples Received - C.gigas High-Low pH Triploid Diploid from Maria Haws Lab • August 20, 2020
• Samples Submitted - Ronits C.gigas Diploid and Triploid Ctenidia to ZymoResearch for WGBS • August 20, 2020
• Assembly Stats - C.bairdi Transcriptomes v2.1 and v3.1 Trinity Stats on Mox • August 19, 2020
• Trimming-FastQC-MultiQC - Robertos C.gigas WGBS FastQ Data with fastp FastQC and MultiQC on Mox • August 18, 2020
• TransDecoder - Hematodinium Transcriptomes v1.6, v1.7, v2.1 and v3.1 on Mox • August 17, 2020
• Assembly Stats - cbaiodinium Transcriptomes v2.1 and v3.1 Trinity Stats on Mox • August 17, 2020
• Transcriptome Assessment - BUSCO Metazoa on Hematodinium v1.6 v1.7 v2.1 and v3.1 on Mox • August 14, 2020
• Transcriptome Annotation - Hematodinium Transcriptomes v1.6 v1.7 v2.1 v3.1 with DIAMOND BLASTx on Mox • August 14, 2020
• qPCR - P.generosa APLP and TIF3s8-1 with cDNA • August 6, 2020

July 2020

• FastQ Read Alignment and Quantification - P.generosa Water Metagenomic Libraries to MetaGeneMark Assembly with Hisat2 on Mox • July 31, 2020
• Primer Design and In-Silico Testing - Geoduck Reproduction Primers • July 30, 2020
• qPCR - Testing P.generosa Reproduction-related Primers • July 29, 2020
• SRA Submission - P.generosa Metagenomics Data • July 27, 2020
• qPCR - Testing P.generosa Reproduction-related Primers • July 23, 2020
• DNA Isolation and Quantification - C.gigas Diploid (Ronit) and Triploid (Nisbet) • July 22, 2020
• SRA Submission - Geoduck Epigenetic Ocean Acidification RNAseq • July 9, 2020
• ENA Submission - Ostrea lurida draft genome Olurida_v081.fa • July 8, 2020

June 2020

• Metagenomics - Data Extractions Using MEGAN6 • June 18, 2020
• Transcriptome Annotation - C.bairdi Transcriptomes v2.1 and v3.1 Using DIAMOND BLASTx on Mox • June 8, 2020
• Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v3.1 • June 5, 2020
• Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v2.1 • June 5, 2020
• Sequence Extractions - C.bairdi Transcriptomes v2.0 and v3.0 Excluding Alveolata with MEGAN6 on Swoose • June 5, 2020
• Transcriptome Annotation - C.bairdi Transcriptomes v2.0 and v3.0 with DIAMOND BLASTx on Mox • June 4, 2020
• Transcriptome Comparison - C.bairdi Transcriptomes Evaluations with DETONATE on Mox • June 1, 2020

May 2020

• Transcriptome Comparison - C.bairdi Transcriptomes Compared with DETONATE on Mox • May 29, 2020
• Transcriptome Annotation - Trinotate C.bairdi Transcriptome-v1.7 on Mox • May 29, 2020
• Transcriptome Comparisons - C.bairdi BUSCO Scores • May 28, 2020
• TransDecoder - C.bairdi Transcriptome v1.7 on Mox • May 27, 2020
• Transcriptome Annotation - C.bairdi Transcriptome v1.7 Using DIAMOND BLASTx on Mox • May 27, 2020
• Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v1.7 • May 27, 2020
• Transcriptome Assembly - C.bairdi All Pooled Arthropoda-only RNAseq Data with Trinity on Mox • May 27, 2020
• Transcriptome Annotation - Trinotate C.bairdi Transcriptome-v3.0 on Mox • May 26, 2020
• Transcriptome Assembly - P.trituberculatus (Japanese blue crab) NCBI SRA BioProject PRJNA597187 Data with Trinity on Mox • May 23, 2020
• SRA Library Assessment - Determine RNAseq Library Strandedness from P.trituberculatus SRA BioProject PRJNA597187 • May 21, 2020
• Tutorial - SRA Toolkit for Data Retrieval and Conversion to FastQ • May 21, 2020
• Transcriptome Annotation - Trinotate C.bairdi Transcriptome-v1.6 on Mox • May 20, 2020
• TransDecoder - C.bairdi Transcriptome v1.6 on Mox • May 19, 2020
• TransDecoder - C.bairdi Transcriptome v3.0 from 20200518 on Mox • May 19, 2020
• Transcriptome Annotation - C.bairdi Transcriptome v1.6 Using DIAMOND BLASTx on Mox • May 19, 2020
• Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v1.6 • May 19, 2020
• Transcriptome Annotation - C.bairdi Transcriptome v3.0 Using DIAMOND BLASTx on Mox • May 19, 2020
• Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v3.0 • May 19, 2020
• Transcriptome Assembly - C.bairdi All Arthropoda-specific RNAseq Data with Trinity on Mox • May 18, 2020
• Data Wrangling - Arthropoda and Alveolata D26 Pool RNAseq FastQ Extractions • May 18, 2020
• Transcriptome Assembly - C.bairdi All Pooled RNAseq Data Without Taxonomic Filters with Trinity on Mox • May 18, 2020
• Transcriptome Annotation - Trinotate C.bairdi Transcriptome v2.0 from 20200502 on Mox • May 13, 2020
• TransDecoder - C.bairdi Transcriptome v2.0 from 20200502 on Mox • May 8, 2020
• Transcriptome Annotation - C.bairdi Transcriptome v2.0 Using DIAMOND BLASTx on Mox • May 8, 2020
• Transcriptome Assessment - BUSCO Metazoa on C.bairdi v2.0 Transcriptome • May 8, 2020
• Transcriptome Assembly - C.bairdi All RNAseq Data Without Taxonomic Filters with Trinity on Mox • May 2, 2020

April 2020

• Transcript Abundance - C.bairdi Alignment-free with Salmon Using 2020-GW Data on Mox • April 29, 2020
• GO to GOslim - C.bairdi Enriched GO Terms from 20200422 DEGs • April 27, 2020
• FastQC-MultiQC - Laura Spencer's QuantSeq Data • April 26, 2020
• Gene Expression - C.bairdi Pairwise DEG Comparisons with 2019 RNAseq using Trinity-Salmon-EdgeR on Mox • April 22, 2020
• RNAseq Reads Extractions - C.bairdi Taxonomic Reads Extractions with MEGAN6 on swoose • April 19, 2020
• Transcript Abundance - C.bairdi Alignment-free with Salmon on Mox for Grace • April 15, 2020
• SRA Submission - C.bairdi RNAseq Data • April 15, 2020
• TrimmingFastQCMultiQC---C.bairdi-RNAseq-FastQ-with-fastp-on-Mox • April 14, 2020
• Taxonomic Assignments - C.bairdi RNAseq Using DIAMOND BLASTx on Mox and MEGAN6 Meganizer on swoose • April 14, 2020
• FastQC-MultiQC - C.bairdi Raw RNAseq from NWGSC • April 14, 2020
• Data Wrangling - Arthropoda and Alveolata Day and Treatment Taxonomic RNAseq FastQ Extractions • April 13, 2020
• Data Received - C.bairdi RNAseq from NWGSC • April 13, 2020
• Transcriptome Annotation - Trinotate C.bairdi MEGAN6 Taxonomic-specific Trinity Assembly on Mox • April 9, 2020
• Transcriptome Annotation - C.bairdi MEGAN Trinity Assembly Using DIAMOND BLASTx on Mox • April 8, 2020
• Transcriptome Annotation - Trinotate Hematodinium MEGAN6 Taxonomic-specific Trinity Assembly on Mox • April 8, 2020
• Transdecoder - Hematodinium MEGAN6 Taxonomic-Specific Reads Assembly from 20200330 • April 7, 2020
• Transdecoder - C.bairdi MEGAN6 Taxonomic-Specific Reads Assembly from 20200330 • April 7, 2020
• Transcriptome Assessment - BUSCO Metazoa on C.bairdi MEGAN Transcriptome • April 7, 2020

March 2020

• Transcriptome Annotation - Hematodinium MEGAN Trinity Assembly Using DIAMOND BLASTx on Mox • March 31, 2020
• Transcriptome Assessment - BUSCO Metazoa on Hematodinium MEGAN Transcriptome • March 31, 2020
• Transcriptome Assembly - Hematodinium with MEGAN6 Taxonomy-specific Reads with Trinity on Mox • March 30, 2020
• Transcriptome Assembly - C.bairdi with MEGAN6 Taxonomy-specific Reads with Trinity on Mox • March 30, 2020
• RNAseq Reads Extractions - C.bairdi Taxonomic Reads Extractions with MEGAN6 on swoose • March 30, 2020
• Transcriptome Annotation - C.bairdi Using DIAMOND BLASTx on Mox and MEGAN6 Meganizer on swoose • March 18, 2020
• Trimming/FastQC/MultiQC - C.bairdi RNAseq FastQ with fastp on Mox • March 18, 2020
• Data Received - C.bairdi RNAseq Data from Genewiz • March 18, 2020
• DNA Isolation and Quantification - C.bairdi Hemocyte Pellets in RNAlater • March 11, 2020
• NanoPore Sequencing - C.bairdi gDNA 6129_403_26 • March 11, 2020
• qPCR - C.bairdi RNA Check for Residual gDNA • March 10, 2020
• Trimming/MultiQC - Methcompare Bisulfite FastQs with fastp on Mox • March 6, 2020
• RNA Isolation and Quantification - C.bairdi RNA from Hemolymph Pellets in RNAlater • March 6, 2020

February 2020

• Data Wrangling - Create Canonical Olurida_v081 Genes FastA • February 28, 2020
• qPCR - C.bairdi RNA Check for Residual gDNA • February 26, 2020
• qPCR - C.bairdi Primer Tests on gDNA • February 25, 2020
• Primer Design - C.bairdi Primers for Checking RNA for Residual gDNA • February 20, 2020
• DNA Isolation & Quantification - C.bairdi RNA from Samples 6212_132_9 6212_334_12 6212_485_26 • February 11, 2020
• RNA Isolation & Quantification - C.bairdi RNA from Samples 6212_132_9 6212_334_12 6212_485_26 • February 11, 2020
• RNA Isolation & Quantification - C.bairdi RNA from Sample 6129_403_26 • February 10, 2020
• DNA Isolation & Quantification - Additional C.bairdi gDNA from Sample 6129_403_26 • February 10, 2020
• DNA Isolation, Quantification, and Gel - C.bairdi gDNA Sample 6129_403_26 • February 10, 2020
• Transcriptome Assessment - BUSCO Metazoa on Hematodinium MEGAN Transcriptome • February 7, 2020
• Transcriptome Assessment - BUSCO Metazoa on C.bairdi MEGAN Transcriptome • February 7, 2020
• Gene Expression - Hematodinium MEGAN6 with Trinity and EdgeR • February 7, 2020
• Gene Expression - C.bairdi MEGAN6 with Trinity and EdgeR • February 7, 2020

January 2020

• Data Wrangling - Arthropoda and Alveolata Day and Treatment Taxonomic RNAseq FastQ Extractions • January 31, 2020
• DNA Isolation and Quantification - C.bairdi Hemocyte Pellets in RNAlater • January 28, 2020
• Transcriptome Annotation - Trinotate Hematodinium MEGAN6 Taxonomic-specific Trinity Assembly on Mox • January 26, 2020
• Transcriptome Annotation - Trinotate C.bairdi MEGAN6 Taxonomic-specific Trinity Assembly on Mox • January 26, 2020
• RNA Isolation and Quantification - C.bairdi Hemocyte Pellets in RNAlater • January 26, 2020
• RNA Isolation and Quantification - C.bairdi Hemocyte Pellets in RNAlater • January 24, 2020
• Transdecoder - Hematodinium MEGAN6 Taxonomic-Specific Reads Assembly from 20200122 • January 23, 2020
• Transdecoder - C.bairdi MEGAN6 Taxonomic-Specific Reads Assembly from 20200122 • January 23, 2020
• Transcriptome Annotation - Hematodinium MEGAN Trinity Assembly Using DIAMOND BLASTx on Mox • January 23, 2020
• Transcriptome Annotation - C.bairdi MEGAN Trinity Assembly Using DIAMOND BLASTx on Mox • January 23, 2020
• RNA Isolation and Quantification - C.bairdi Hemocyte Pellets in RNAlater Troubleshooting • January 23, 2020
• DNA Quality Assessment - Agarose Gel for C.bairdi 20102558-2729 gDNA from 20200122 • January 22, 2020
• Data Wrangling - Arthropoda and Alveolata Taxonomic RNAseq FastQ Extractions • January 22, 2020
• DNA Isolation - C.bairdi 20102558-2729 EtOH-preserved Tissue via Three Variations Using Quick DNA-RNA MicroPrep Kit • January 22, 2020
• Transcriptome Assembly - Hematodinium with MEGAN6 Taxonomy-specific Reads with Trinity on Mox • January 22, 2020
• Transcriptome Assembly - C.bairdi with MEGAN6 Taxonomy-specific Reads with Trinity on Mox • January 22, 2020
• DNA Isolation and Quantification - C.bairdi Hemolymph Pellets in RNAlater • January 17, 2020
• RNA Isolation and Quantification - C.bairdi Hemolymph Pellets in RNAlater • January 17, 2020
• RNAseq Reads Extractions - C.bairdi Taxonomic Reads Extractions with MEGAN6 on swoose • January 14, 2020
• Lab Maintenance - Cluster UPS Battery Replacement • January 10, 2020
• NanoPore Sequencing - C.bairdi gDNA Sample 20102558-2729 • January 9, 2020
• DNA Quality Assessment - Agarose Gel and NanoDrop on C.bairdi gDNA • January 9, 2020
• DNA Isolation and Quantification - C.bairdi gDNA from EtOH Preserved Tissue • January 8, 2020
• NanoPore Sequencing - Initial NanoPore MinION Lambda Sequencing Test • January 7, 2020
• Transcriptome Annotation - C.bairdi Using DIAMOND BLASTx on Mox and MEGAN6 Meganizer • January 3, 2020
• Reagent Prep - RNA Pico Ladder Aliquoting and Testing • January 2, 2020

2019

</ul>

December 2019

• Transcriptome Annotation - C.bairdi Trinity Assembly Trinotate on Mox • December 25, 2019
• Transcriptome Annotation - C.bairdi Trinity Assembly BLASTx on Mox • December 24, 2019
• Transdecoder - C.bairdi De Novo Transcriptome from 20191218 on Mox • December 20, 2019
• Transcriptome Assembly - C.bairdi Trimmed RNAseq Using Trinity on Mox • December 18, 2019
• Trimming/FastQC/MultiQC - C.bairdi RNAseq FastQ with fastp on Mox • December 18, 2019
• Data Wrangling - Olurida_v081 UTR GFFs and Intergenic, Intron BED files • December 14, 2019
• Samples Received - Pacific Oyster Tissues from Hawaii (Maria Haws) from High and Low pCO2 • December 10, 2019
• Data Wrangling - Renaming, Splitting, and Feature Counts of Updated Pgenerosa_v074 GenSAS Merged GFF • December 3, 2019
• PCR - Crassostrea gigas and sikamea Mantle gDNA from Marinelli Shellfish Company • December 3, 2019

November 2019

• Samples Received - C.bairdi Hemolymph and Tissue in Ethanol from Pam Jensen • November 27, 2019
• qPCR - Geoduck hemolymph and hemocyte cDNA with vitellogenin primers • November 27, 2019
• Reverse Transcription - P.generosa DNased Hemolypmh and Hemocyte RNA from 20191125 • November 26, 2019
• RNA Isolation and Quantification - Geoduck hemolymph and hemocyte samples • November 25, 2019
• PCR - Crassostrea gigas and sikamea Mantle gDNA from Marinellie Shellfish Company - No Multiplex • November 21, 2019
• PCR - Crassostrea gigas and sikamea Mantle gDNA from Marinelli Shellfish Company • November 21, 2019
• Data Wrangling - Rename Pgenerosa_v074 Bismark Coverage Files Scaffold Names • November 20, 2019
• PCR - Crassostrea gigas and sikamea Mantle gDNA from Marinelli Shellfish Company • November 19, 2019
• DNA Isolation and Quantification - Crassostrea gigas and Crassostrea sikamea Mantle Tissue from Marinelli Shellfish Company • November 19, 2019
• Data Wrangling - Additional Features Stats for Panopea-generosa-v1.0 • November 6, 2019
• Data Wrangling - Rename Pgenerosa_v074 Files and Scaffolds • November 5, 2019

October 2019

• Data Wrangling - Splitting BAM by Size for Upload to OSF • October 31, 2019
• Samples Received - Marinelli Shellfish Company C.gigas and C.sikamea Oysters • October 30, 2019
• Data Wrangling - Create Panopea-generosa-vv0.74.a4 Intron and Intergenic BED Files • October 30, 2019
• Genome Feature Counts - Panopea-generosa-vv0.74.a4 • October 29, 2019
• FastQC-MultiQC - C.bairdi RNAseq Day 12 26 Infected Uninfected • October 24, 2019
• Data Received - C.bairdi RNAseq Day9-12-26 Infected-Uninfected • October 24, 2019
• Lab Maintenance - Cluster UPS Battery Replacement • October 22, 2019
• Metagenomics Annotation - P.generosa Water Samples with MEGAN6 • October 14, 2019
• Data Received - C.bairdi RNAseq Day9-12-26 Infected-Uninfected • October 3, 2019

September 2019

• Genome Annotation - Pgenerosa_v074 a4 Using GenSAS • September 28, 2019
• Metagenomics Annotation - P.generosa Water Samples Using DIAMOND BLASTx on Mox • September 25, 2019
• Trimming/FastQC/MultiQC - P.generosa EPI FastQs with FASTP on Mox • September 23, 2019
• SRA Submission - Hollie's Juvenile OA BS-seq Data • September 18, 2019
• Data Wrangling - Pgenerosa_v074.a3 Annotation Genome Repeats Compostion • September 5, 2019
• Data Wrangling - Pgenerosa_v074.a3 Annotation Genome Feature Sequence Lengths • September 4, 2019

August 2019

• Data Wrangling - Panopea generosa Genome Feature Sequence Lengths • August 26, 2019
• Data Wrangling - Create a CpG GFF from Pgenerosa_v074 using EMBOSS fuzznuc on Swoose • August 21, 2019
• Genome Annotation - Pgenerosa_v074 MAKER on Mox with Stringtie Transcripts GFF • August 19, 2019
• Genome Comparison - Pgenerosa_v074 vs Pgenerosa_v070 with MUMmer Promer on Mox • August 13, 2019
• Genome Comparison - Pgenerosa_v074 vs S.glomerata NCBI with MUMmer Promer on Mox • August 13, 2019
• Genome Comparison - Pgenerosa_v074 vs M.yessoensis NCBI with MUMmer Promer on Mox • August 13, 2019
• Genome Comparison - Pgenerosa_v074 vs H.sapiens NCBI with MUMmer Promer on Mox • August 13, 2019
• Genome Comparison - Pgenerosa_v074 vs C.virginica NCBI with MUMmer Promer on Mox • August 13, 2019
• Genome Comparison - Pgenerosa_v074 vs C.gigas NCBI with MUMmer Promer on Mox • August 13, 2019
• Genome Comparison - Pgenerosa_v074 vs Pgenerosa_v070 with MUMmer on Mox • August 7, 2019
• Genome Comparison - Pgenerosa_v074 vs Pgenerosa_v074 with MUMmer on Mox • August 7, 2019
• Genome Comparison - Pgenerosa_v074 vs S.glomerata NCBI with MUMmer on Mox • August 7, 2019
• Genome Comparison - Pgenerosa_v074 vs M.yessoensis NCBI with MUMmer on Mox • August 7, 2019
• Genome Comparison - Pgenerosa_v074 vs H.sapiens NCBI with MUMmer on Mox • August 7, 2019
• Genome Comparison - Pgenerosa_v074 vs C.gigas NCBI with MUMmer on Mox • August 7, 2019
• Genome Comparison - Pgenerosa_v074 vs C.virginica NCBI with MUMmer on Mox • August 6, 2019
• RepeatMasker - Pgenerosa_v070 for Transposable Element ID on Roadrunner • August 6, 2019

July 2019

• Data Wrangling - FastA Splitting With faSplit • July 31, 2019
• Data Summary - P.generosa Transcriptome Assemblies Stats • July 29, 2019
• Transcriptome Compression - P.generosa Transcriptome Assemblies Using CD-Hit-est on Mox • July 29, 2019
• Genome Annotation - Pgenerosa_v074 Transcript Isoform ID with Stringtie on Mox • July 23, 2019
• Genome Annotation - Pgenerosa_v070 Transcript Isoform ID with Stringtie on Mox • July 23, 2019
• Genome Annotation - Pgenerosa_v074 Hisat2 Transcript Isoform Index • July 23, 2019
• Genome Annotation - Pgenerosa_v070 Hisat2 Transcript Isoform Index • July 23, 2019
• Genome Annotation - Pgenerosa_v070 and v074 Top 18 Scaffolds Feature Count Comparisons • July 22, 2019
• Genome Annotation - O.lurida 20190709-v081 Transcript Isoform ID with Stringtie on Mox • July 16, 2019
• Genome Annotation - O.lurida 20190709-v081 Hisat2 Transcript Isoform Index • July 16, 2019
• Genome Assessment - BUSCO Metazoa on Pgenerosa_v074 on Mox • July 10, 2019
• Genome Assessment - BUSCO Metazoa on Pgenerosa_v70 on Mox • July 10, 2019
• Genome Annotation - Pgenerosa_v071 Using GenSAS • July 10, 2019
• Genome Annotation - Pgenerosa_v074 Using GenSAS • July 10, 2019
• Genome Annotation - Olurida_v081 with MAKER and Tissue-specific Transcriptomes on Mox • July 9, 2019
• Genome Annotation - Pgenerosa_v074 MAKER on Mox • July 1, 2019

June 2019

• Transcriptome Annotation - Geoduck Larvae Day5 EPI99 with Transdecoder on Mox • June 27, 2019
• Transcriptome Annotation - Geoduck Super Low OA EPI116 with Transdecoder on Mox • June 27, 2019
• Transcriptome Annotation - Geoduck Juvenile Super Low OA EPI115 with Transdecoder on Mox • June 27, 2019
• Transcriptome Annotation - Geoduck Juvenile Ambient OA EPI124 with Transdecoder on Mox • June 27, 2019
• Transcriptome Annotation - Geoduck Juvenile Ambient OA EPI123 with Transdecoder on Mox • June 27, 2019
• Transcriptome Annotation - Geoduck Gonad with Transdecoder on Mox • June 27, 2019
• Transcriptome Annotation - Geoduck Ctenidia with Transdecoder on Mox • June 27, 2019
• RepeatModeler - Pgenerosa_v074 for MAKER Annotation on Emu • June 26, 2019
• RepeatMasker - Pgenerosa_v074 for Transposable Element ID on Roadrunner • June 26, 2019
• Data Received - C.virginica Mantle MBD-BSseq from ZymoResearch • June 26, 2019
• Data Wrangling - FastA Subsetting of Pgenerosa_v070.fa Using samtools faidx • June 25, 2019
• Genome Annotation - O.lurida (v081) Transcript Isoform ID with Stringtie on Mox • June 25, 2019
• Genome Annotation - O.lurida (v081) Hisat2 Transcript Isoforms Index • June 25, 2019
• Metagenomics - Refining Anvio Binning • June 19, 2019
• Metagenomics - Taxonomic Diversity and Sequencing Coverage with MEGAHIT BLASTx and Krona Plots • June 12, 2019

May 2019

• Data Wrangling - Create Pgenerosa_v070 GFFs • May 23, 2019
• Sample Submission - Tanner Crab Infected vs Uninfected RNAseq • May 21, 2019
• Metagenomics - BLASTx of Individual Water Sample MEGAHIT Assemblies on Mox • May 16, 2019
• Library Decisions - C.bairdi RNAs for Library Pools • May 14, 2019
• FastQC-MultiQC - Additional C.gigas WGBS Sequencing Data from Genewiz Received 20190501 • May 1, 2019
• Data Received - Additional C.gigas Whole Genome Bisulfite Sequencing Data from Genewiz • May 1, 2019

April 2019

• RNA Isolation and Quantification - C.bairdi Hemolymph Pellet in RNAlater • April 30, 2019
• SRA Submission - P.generosa 10x Genomics Sequencing Data • April 24, 2019
• Data Analysis - C.virginica MBD Sequencing Coverage • April 18, 2019
• Metagenomics Annotation - P.generosa Water Samples Using BLASTn on Mox and KronaTools Visualization to Compare pH Treatments • April 16, 2019
• Metagenomics Gene Prediction - P.generosa Water Samples Using MetaGeneMark on Mox to Compare pH Treatments • April 16, 2019
• FastQC - WGBS Sequencing Data from Genewiz Received 20190408 • April 15, 2019
• Metagenome Assemblies - P.generosa Water Samples Trimmed HiSeqX Data Using Megahit on Mox to Compare pH Treatments • April 15, 2019
• RNA Isolation and Quantification - Crab Hemolypmh Using Quick-DNA-RNA Microprep Plus Kit • April 11, 2019
• Transcriptome Assembly - Geoduck Tissue-specific Assembly Larvae Day5 EPI99 with HiSeq and NovaSeq Data on Mox • April 9, 2019
• Transcriptome Assembly - Geoduck Tissue-specific Assembly Gonad HiSeq and NovaSeq Data on Mox • April 9, 2019
• Transcriptome Assembly - Geoduck Tissue-specific Assembly Juvenile Ambient OA EPI124 with HiSeq and NovaSeq Data on Mox • April 9, 2019
• Transcriptome Assembly - Geoduck Tissue-specific Assembly Juvenile Ambient OA EPI123 with HiSeq Data on Mox • April 9, 2019
• Transcriptome Assembly - Geoduck Tissue-specific Assembly Juvenile Super Low OA EPI116 with HiSeq and NovaSeq Data on Mox • April 9, 2019
• Transcriptome Assembly - Geoduck Tissue-specific Assembly Juvenile Super Low OA EPI115 with HiSeq Data on Mox • April 9, 2019
• Transcriptome Assembly - Geoduck Tissue-specific Assembly Ctenidia with HiSeq and NovaSeq Data on Mox • April 9, 2019
• Data Management - Whole Genome Bisulfite Sequencing Data from Genewiz Received • April 8, 2019
• Metagenomics - P.generosa Water Sample Assembly Comparisons with Quast • April 8, 2019
• Metagenomics - Geoduck Water Sample Assembly Comparisons with MetaQuast • April 3, 2019
• Metagenomics - Taxonomic Diversity Comparisons from Geoduck Water with Anvio on Mox • April 1, 2019

March 2019

• Metagenome Assemblies - P.generosa Water Samples Trimmed HiSeqX Data Using Megahit on Mox • March 27, 2019
• Transposable Element Mapping - Crassostrea gigas Genome v9 Using RepeatMasker 4.07 on Roadrunner • March 27, 2019
• Sample Submission - Lotterhos C.virginica Mantle MBD DNA to ZymoResearch for BSseq • March 26, 2019
• Data Management - SRA Submission Panopea generosa Day 5 Larvae RNAseq • March 26, 2019
• Metagenomics - Taxonomic Diversity from Geoduck Water with BLASTn and Krona Plots • March 25, 2019
• Metagenomics - Taxonomic Diversity from Geoduck Water with BLASTp and Krona plots • March 25, 2019
• MBD Enrichment - DNA Quantification of C.virginica MBD Samples from 20190312 • March 19, 2019
• Transcriptome Annotation - Geoduck Juvenile Day 5 with Trinotate on Mox • March 18, 2019
• Transcriptome Annotation - Geoduck Heart with Trinotate on Mox • March 18, 2019
• Transcriptome Annotation - Geoduck Gonad with Trinotate on Mox • March 18, 2019
• Transcriptome Annotation - Geoduck Ctenidia with Trinotate on Mox • March 18, 2019
• Transcriptome Annotation - Geoduck Heart with BLASTx on Mox • March 18, 2019
• Transcriptome Annotation - Geoduck Gonad with BLASTx on Mox • March 18, 2019
• Transcriptome Annotation - Geoduck Ctenidia with BLASTx on Mox • March 18, 2019
• Transcriptome Annotation - Geoduck Juvenile Day 5 with BLASTx on Mox • March 18, 2019
• Transcriptome Annotation - Geoduck Juvenile Day 5 with Transdecoder on Mox • March 18, 2019
• Transcriptome Annotation - Geoduck Heart with Transdecoder on Mox • March 18, 2019
• Transcriptome Annotation - Geoduck Gonad with Transdecoder on Mox • March 18, 2019
• Transcriptome Annotation - Geoduck Ctenidia with Transdecoder on Mox • March 18, 2019
• Methylation Analysis - C.virginica Gonad MBD with Varying Read Subsets with Bismark on Mox • March 13, 2019
• Data Management - Create C.virginica Bisulfite Genome with Bismark on Mox • March 12, 2019
• MBD Enrichment - Ethanol Precipitation of C.virginica MBD samples • March 12, 2019
• MBD Enrichment - C.virginica Sheared Mantle DNA from 20190306 • March 11, 2019
• MBD Enrichment - C.virginica Sheared Mantle DNA from 20190306 • March 7, 2019
• DNA Shearing & Bioanalyzer - Lotterhos C.virginica Mantle gDNA from 2018114 • March 6, 2019
• Agarose Gel - Lotterhos C.virginica Mantle DNA from 20181114 • March 5, 2019
• Data Management - Data Migration and Drive Expansion on Gannet • March 4, 2019
• Genome Assessment - BUSCO Metazoa on P.generosa v071 on Mox • March 2, 2019

February 2019

• Genome Annotation - Pgenerosa_v070 MAKER on Mox • February 28, 2019
• Data Wrangling - CpG OE Calculations on C.virginica Genes • February 26, 2019
• Methylation Analysis - P.generosa Bismark on Mox • February 22, 2019
• Methylation Analysis - O.lurida Bismark on Mox • February 22, 2019
• Methylation Analysis - C.virginica • February 22, 2019
• Methylation Analysis - C.gigas Bismark on Mox • February 22, 2019
• Data Management - Create C.virginica Bisulfite Genome wit Bismark on Mox • February 21, 2019
• Data Management - Create C.gigas Bisulfite Genome with Bismark on Mox • February 21, 2019
• Data Management - Create Geoduck Bisulfite Genomes with Bismark on Mox • February 21, 2019
• Transcriptome Assembly - Geoduck Tissue-specific Assembly Juvenile Day 5 • February 15, 2019
• Transcriptome Assembly - Geoduck Tissue-specific Assembly Heart • February 15, 2019
• Transcriptome Assembly - Geoduck Tissue-specific Assembly Gonad • February 15, 2019
• Transcriptome Assembly - Geoduck Tissue-specific Assembly Ctenidia • February 15, 2019
• Genome Annotation - Pgenerosa_v71 with MAKER on Mox • February 13, 2019
• Sequence Subsetting - Pgenerosa_v70 Genome Assembly with faidx • February 11, 2019
• Samples Submitted - Robertos C.gigas DNA for Whole Genome Bisulfite Sequencing (Genewiz) • February 7, 2019

January 2019

• Samples Received - C.virginica DNA and Tissues from Lotterhos Lab • January 29, 2019
• DNA Isolation and Quantification - Ronit's C.gigas Ploidy Ctenidia • January 23, 2019
• DNA Isolation - C.gigas Ploidy Experiment Ctenidia • January 17, 2019
• Annotation - Olurida_v081 MAKER BUSCO Metazoa Augustus Training on Mox • January 15, 2019
• Annotation - Geoduck Genome with MAKER Submitted to Mox • January 15, 2019
• Annotation - Olurida_v081 MAKER BUSCO (eukaryota_odb9) Augustus Training Submitted to Mox • January 14, 2019
• Annotation - Olurida_v081 MAKER Functional Annotations on Mox • January 9, 2019
• Annotation - Olurida_v081 MAKER Proteins BLASTp on Mox • January 8, 2019
• Annotation - Olurida_v081 MAKER Proteins InterProScan5 on Mox • January 8, 2019
• Annotation - Olurida_v081 MAKER ID Mapping • January 8, 2019
• Gene Prediction - HiSeqX Metagenomics from Geoduck Water Using MetaGeneMark on Mox • January 3, 2019
• Metagenome Assembly - P.generosa Water Sample Trimmed HiSeqX Data Using Megahit on Mox • January 2, 2019
• VCF Splitting - C.virginica VCF Using BCFtools • January 2, 2019

2018

</ul>

December 2018

• DNA Isolation - C.gigas Ploidy Experiment Ctenidia • December 20, 2018
• Repeat Library Construction - P.generosa RepeatModeler v1.0.11 • December 19, 2018
• qPCR - Relative mitochondrial abundance in C.gigas diploids and triploids subjected to acute heat stress via COX1 • December 17, 2018
• BLASTx - Clupea pallasii (Pacific herring) liver and testes transcriptomes on Mox • December 12, 2018
• FastQC and Trimming - Metagenomics (Geoduck) HiSeqX Reads from 20180809 • December 11, 2018
• Primer Design - Gigas COX1 using Primer3 • December 11, 2018
• qPCR - Geoduck gonad cDNA with vitellogenin primers • December 6, 2018
• Reverse Transcription - Geoduck gonad RNA pool • December 6, 2018

November 2018

• Primer Design - Geoduck Vitellogenin using Primer3 • November 29, 2018
• Annotation - Olurida_v081 MAKER on Mox • November 27, 2018
• Annotation - Geoduck Transcritpome with TransDecoder • November 21, 2018
• Reverse Transcription - Ronit's C.gigas DNased RNA from 20181115 • November 20, 2018
• RNA Quantification - Ronit's C.gigas DNased RNA from 20181115 • November 20, 2018
• qPCR - Ronit's DNased C.gigas RNA with Elongation Factor Primers • November 15, 2018
• DNase - Ronit's C.gigas Ctenidia RNA • November 15, 2018
• DNA Isolation and Quantification - Lotterhos C.virginica Mantle DNA • November 14, 2018
• Computing - Install NCBI nr nt BLAST Database on Mox • November 14, 2018
• My New Notebook • November 8, 2018

October 2018

• Repeat Library Construction - O.lurida RepeatModeler v1.0.11 • October 22, 2018
• qPCRs - Ronit's C.gigas ploidy/dessication/heat stress cDNA (1:5 dilution) • kubu4 • October 18, 2018
• Samples Received - Crassostrea virginica (Eastern oyster) tissue from Lotterhos Lab (Northeastern University) • kubu4 • October 17, 2018
• Reverse Transcription - Ronit's C.gigas DNased ctenidia RNA • kubu4 • October 17, 2018
• qPCR - Ronit’s DNAsed C.gigas Ploidy/Dessication RNA with elongation factor primers • kubu4 • October 17, 2018
• qPCR – C.gigas primer and gDNA tests with 18s and EF1 primers • kubu4 • October 16, 2018
• qPCR - Ronit's DNAsed C.gigas Ploidy/Dessication RNA with 18s primers • kubu4 • October 16, 2018
• DNase Treatment - Ronit's C.gigas Ploiyd/Dessication Ctenidia RNA • kubu4 • October 16, 2018
• RNA Quantification - Ronit's C.gigas Ploidy/Dessication RNA • kubu4 • October 16, 2018
• Data Received - Chionoecetes bairdi RNAseq & FastQC Analysis • kubu4 • October 15, 2018
• VCF Splitting with bcftools • kubu4 • October 15, 2018
• RNA Isolation - Tanner Crab Hemolymph Pellet in RNAlater using TriReagent • kubu4 • October 9, 2018
• RNA Isolation - Ronit's C.gigas diploid/triploid dessication/heat shock ctenidia tissues • kubu4 • October 3, 2018
• SRA Submission - Olymia oyster Whole Genome BS-seq Data • kubu4 • October 3, 2018
• Installation - Microsoft Machine Learning Server (Microsoft R Open) on Emu/Roadrunner R Studio Server • kubu4 • October 2, 2018
• Ubuntu – Fix “No Video Signal” Issue on Emu • kubu4 • October 2, 2018

September 2018

• Transcriptome Alignment & Bedgraph – Olympia oyster transcriptome with Olurida_v080 genome assembly • kubu4 • September 27, 2018
• Bedgraph – Olympia oyster transcriptome with Olurida_v081 genome assembly • kubu4 • September 26, 2018
• Transcriptome Alignment – Olympia oyster RNAseq reads aligned to genome with HISAT2 • kubu4 • September 25, 2018
• Bedgraph - Olympia oyster transcriptome (FAIL) • kubu4 • September 24, 2018
• Transcriptome Alignment - Olympia oyster Trinity transcriptome aligned to genome with Bowtie2 • kubu4 • September 20, 2018
• Transcriptome Assembly - Olympia oyster RNAseq Data with Trinity • kubu4 • September 19, 2018
• DNA Methylation Analysis – Olympia Oyster Whole Genome BSseq Bismark Pipeline MethylKit Comparison • kubu4 • September 18, 2018
• RNA Isolation - Lyophilized Tanner Crab Hemolymph in RNAlater • kubu4 • September 17, 2018
• DNA Methylation Analysis - Olympia Oyster Whole Genome BSseq Bismark Pipeline Comparison • kubu4 • September 13, 2018
• DNA Quantification - Sea Lice DNA from 20180523 • kubu4 • September 12, 2018
• TrimGalore/FastQC/MultiQC - C.virginica Oil Spill MBDseq Concatenated Sequences • kubu4 • September 11, 2018
• Sequencing Data Analysis - C.virginica Oil Spill MBDseq Concatenation & FastQC • kubu4 • September 10, 2018
• DNA Methylation Analysis - Olympia oyster BSseq MethylKit Analysis • kubu4 • September 4, 2018
• Transcriptome Assembly - Geoduck RNAseq data • kubu4 • September 4, 2018

August 2018

• FastQC/MultiQC/TrimGalore/MultiQC/FastQC/MultiQC - O.lurida WGBSseq for Methylation Analysis • kubu4 • August 30, 2018
• Transposable Element Mapping – Crassostrea virginica Genome, Cvirginica_v300, using RepeatMasker 4.07 • kubu4 • August 28, 2018
• Assembly Stats – Geoduck Hi-C Final Assembly Comparison • kubu4 • August 23, 2018
• DNA Methylation Analysis - Bismark Pipeline on All Olympia oyster BSseq Datasets • kubu4 • August 16, 2018
• Data Received - Geoduck Metagenome HiSeqX Data • kubu4 • August 9, 2018
• RNA Isolation & Quantificaiton - Tanner Crab Hemolymph • kubu4 • August 9, 2018
• Genome Annotation – Olympia oyster genome annotation results #02 • kubu4 • August 8, 2018
• Genome Annotation - Olympia oyster genome annotation results #01 • kubu4 • August 8, 2018
• Genome Annotation – Olympia oyster genome complete - brief note • kubu4 • August 7, 2018
• Genome Annotation - Olympia oyster genome using WQ-MAKER Instance on Jetstream • kubu4 • August 7, 2018
• Bioanalyzer - Tanner Crab RNA Isolated with RNeasy Plus Mini Kit • kubu4 • August 1, 2018

July 2018

• RNA Cleanup - Tanner Crab RNA • kubu4 • July 31, 2018
• RNA Isolation - Tanner Crab Hemolymph Using RNeasy Plus Mini Kit • kubu4 • July 31, 2018
• Mox – Over quota: Olympia oyster genome annotation progress (using Maker 2.31.10) • kubu4 • July 30, 2018
• RNA Cleanup - Tanner Crab RNA Pools • kubu4 • July 19, 2018
• Mox - Olympia oyster genome annotation progress (using Maker 2.31.10) • kubu4 • July 11, 2018
• Mox - Password-less SSH! • kubu4 • July 11, 2018
• Ubuntu - Fix "No Video Signal" Issue on Emu/Roadrunner • kubu4 • July 5, 2018
• Transposable Element Mapping – Olympia Oyster Genome Assembly, Olurida_v081, using RepeatMasker 4.07 • kubu4 • July 3, 2018

June 2018

• Library Construction - Geoduck Water Filter Metagenome with Nextera DNA Flex Kit (Illumina) • kubu4 • June 6, 2018

May 2018

• BS-seq Mapping – Olympia oyster bisulfite sequencing: Bismark Continued • kubu4 • May 31, 2018
• Transposable Element Mapping – Crassostrea virginica NCBI Genome Assembly using RepeatMasker 4.07 • kubu4 • May 29, 2018
• Read Mapping – Olympia oyster 2bRAD Data with Bowtie2 (on Mox) • kubu4 • May 26, 2018
• Transposable Element Mapping - Olympia Oyster Genome Assembly using RepeatMasker 4.07 • kubu4 • May 23, 2018
• DNA Received - Sea lice DNA from Cris Gallardo-Escarate at Universidad de Concepción • kubu4 • May 23, 2018
• Software Installation – RepeatMasker v4.0.7 on Emu/Roadrunner Continued • kubu4 • May 23, 2018
• Software Installation - RepeatMasker v4.0.7 on Emu/Roadrunner • kubu4 • May 22, 2018
• TrimGalore/FastQC/MultiQC – TrimGalore! RRBS Geoduck BS-seq FASTQ data (directional) • kubu4 • May 16, 2018
• FastQC - RRBS Geoduck BS-seq FASTQ data • kubu4 • May 16, 2018
• TrimGalore/FastQC/MultiQC – TrimGalore! RRBS Geoduck BS-seq FASTQ data • kubu4 • May 16, 2018
• Data Management - Illumina NovaSeq Geoduck Genome Sequencing • kubu4 • May 16, 2018
• Assembly - Geoduck Hi-C Assembly Subsetting • kubu4 • May 12, 2018
• Read Mapping - Mapping Illumina Data to Geoduck Genome Assemblies with Bowtie2 • kubu4 • May 9, 2018
• BS-seq Mapping - Olympia oyster bisulfite sequencing: TrimGalore > FastQC > Bismark • kubu4 • May 8, 2018
• Assembly & Stats - SparseAssembler (k95) on Geoduck Sequence Data > Quast for Stats • kubu4 • May 1, 2018

April 2018

• Assembly Stats - Geoduck Genome Assembly Comparisons w/Quast - SparseAssembler, SuperNova, Hi-C • kubu4 • April 30, 2018
• Assembly Stats - Geoduck Hi-C Assembly Comparison • kubu4 • April 30, 2018
• DNA Isolation & Quantification - Metagenomics Water Filters • kubu4 • April 26, 2018
• Total Alkalinity Calculations - Yaamini's Ocean Chemistry Samples • kubu4 • April 24, 2018
• Assembly – SparseAssembler (k 111) on Geoduck Sequence Data • kubu4 • April 23, 2018
• Assembly – SparseAssembler (k 131) on Geoduck Sequence Data • kubu4 • April 22, 2018
• Data Management - Geoduck Phase Genomics Hi-C Data • kubu4 • April 21, 2018
• Kmer Estimation – Kmergenie (k 301) on Geoduck Sequence Data • kubu4 • April 21, 2018
• Kmer Estimation – Kmergenie Tweaks on Geoduck Sequence Data • kubu4 • April 19, 2018
• Kmer Estimation - Kmergenie on Geoduck Sequence Data (default settings) • kubu4 • April 19, 2018
• Assembly Stats - Quast Stats for Geoduck SparseAssembler Job from 20180405 • kubu4 • April 15, 2018
• Data Management - SRA Submission LSU C.virginica Oil Spill MBD BS-seq Data • kubu4 • April 12, 2018
• TrimGalore/FastQC/MultiQC - Trim 10bp 5'/3' ends C.virginica MBD BS-seq FASTQ data • kubu4 • April 11, 2018
• DNA Isolation & Quantification - Metagenomics Water Filters • kubu4 • April 11, 2018
• TrimGalore/FastQC/MultiQC - 2bp 3' end Read 1s Trim C.virginica MBD BS-seq FASTQ data • kubu4 • April 11, 2018
• TrimGalore/FastQC/MultiQC - 14bp Trim C.virginica MBD BS-seq FASTQ data • kubu4 • April 10, 2018
• TrimGalore/FastQC/MultiQC - Auto-trim C.virginica MBD BS-seq FASTQ data • kubu4 • April 9, 2018
• FastQC/MultiQC - C. virginica MBD BS-seq Data • kubu4 • April 9, 2018
• Genome Assembly - SparseAssembler Geoduck Genomic Data, kmer=101 • kubu4 • April 5, 2018
• Gunzip - BGI HiSeq Geoduck Genome Sequencing Data • kubu4 • April 5, 2018
• Gunzip - Trimmed Illumina Geoduck HiSeq Genome Sequencing Data • kubu4 • April 4, 2018
• DNA Isolation & Quantification – Geoduck larvae metagenome filter rinses • kubu4 • April 3, 2018
• Titrations - Yaamini's Seawater Samples • kubu4 • April 3, 2018
• Titrations - Yaamini's Seawater Samples • kubu4 • April 2, 2018
• TrimGalore!/FastQC/MultiQC - Illumina HiSeq Genome Sequencing Data Continued • kubu4 • April 1, 2018

March 2018

• Data Received - Crassostrea virginica MBD BS-seq from ZymoResearch • kubu4 • March 29, 2018
• FastQC/MultiQC – Illumina HiSeq Genome Sequencing Data • kubu4 • March 28, 2018
• TrimGalore!/FastQC/MultiQC - Illumina HiSeq Genome Sequencing Data • kubu4 • March 28, 2018
• FastQC/MultiQC - BGI Geoduck Genome Sequencing Data • kubu4 • March 27, 2018
• Titrations - Hollie's Seawater Samples • kubu4 • March 27, 2018
• Assembly - Geoduck NovaSeq using SparseAssembler kmer = 101 • kubu4 • March 27, 2018
• Assembly - Geoduck NovaSeq using SparseAssembler (TL;DR - it worked!) • kubu4 • March 22, 2018
• Titrations - Hollie's Seawater Samples • kubu4 • March 20, 2018
• DNA Isolation & Quantification - Geoduck larvae metagenome filter rinses • kubu4 • March 20, 2018
• Titrations - Hollie's Seawater Samples • kubu4 • March 19, 2018
• Titrations - Hollie's Seawater Samples • kubu4 • March 16, 2018
• Samples Received - Geoduck larvae metagenome filter rinses • kubu4 • March 13, 2018
• Assembly - Geoduck NovaSeq using SparseAssembler (failed) • kubu4 • March 8, 2018
• Progress Report - Titrator • kubu4 • March 6, 2018

February 2018

• Ubuntu Installation - Convert Apple Xserve "bigfish" to Ubuntu • kubu4 • February 28, 2018
• Hardware Upgrades - USB 3.0 PCI Card and 1TB SSD in Woodpecker • kubu4 • February 28, 2018
• Samples Received - Triploid Crassostrea gigas from Nisbet Oyster Company • kubu4 • February 28, 2018
• NovaSeq Assembly - The Struggle is Real - Real Annoying! • kubu4 • February 21, 2018
• Assembly - Geoduck Illumina NovaSeq SOAPdenovo2 on Mox (FAIL) • kubu4 • February 19, 2018
• Ethanol Precipitation & DNA Quantification - C. virginica MBD DNA from Yaamini • kubu4 • February 7, 2018
• NovaSeq Assembly - Trimmed Geoduck NovaSeq with Meraculous • kubu4 • February 5, 2018
• Titrator Setup - Functional Methods & Data Exports • kubu4 • February 1, 2018

January 2018

• Adapter Trimming and FASTQC - Illumina Geoduck Novaseq Data • kubu4 • January 25, 2018
• Software Install - 10x Genomics Supernova on Mox (Hyak) • kubu4 • January 22, 2018
• Samples Submitted - C. virginica gDNA, MBD, and MspI to Qiagen • kubu4 • January 16, 2018
• Assembly Comparisons – Oly Assemblies Using Quast • kubu4 • January 16, 2018
• DNA Quantification - MspI-digested Crassostrea virginica gDNA • kubu4 • January 11, 2018
• Phenol:Chloroform Extractions and EtOH Precipitations - MspI Digestions of C.virginica DNA from Earlier Today • kubu4 • January 11, 2018
• Restriction Digestion - MspI on Crassotrea virginica gDNA • kubu4 • January 11, 2018
• DNA Quantification - C.virginica MBD-enriched DNA • kubu4 • January 10, 2018
• MBD Enrichment – Crassostrea virginica Sheared DNA Day 3 • kubu4 • January 10, 2018
• MBD Enrichment – Crassostrea virginica Sheared DNA Day 2 • kubu4 • January 10, 2018
• MBD Enrichment - Crassostrea virginica Sheared DNA Day 1 • kubu4 • January 8, 2018

2017

</ul>

December 2017

• Tissue Sampling - Crassostrea virginica Tissues for Archiving • kubu4 • December 13, 2017
• Software Install - MSMTP For Email Notices of Bash Job Completion on Emu (Ubuntu) • kubu4 • December 13, 2017
• Samples Submitted - Pulverized Geoduck Tissues to Illumina for More 10x Genomics Sequencing • kubu4 • December 12, 2017
• DNA Sonication & Bioanalzyer - C. virginica gDNA for MeDIP • kubu4 • December 11, 2017
• DNA Isolation & Quantification - Crassostrea virginica Mantle gDNA • kubu4 • December 11, 2017

November 2017

• Genome Assembly – Olympia Oyster Illumina & PacBio Using PB Jelly w/BGI Scaffold Assembly • kubu4 • November 30, 2017
• Troubleshooting – PB Jelly Install on Emu Continued • kubu4 • November 30, 2017
• Samples Submitted - Geoduck Tissues to Illumina for More 10x Genomics Sequencing • kubu4 • November 21, 2017
• Troubleshooting - PB Jelly Install on Emu • kubu4 • November 21, 2017
• DNA Isolation & Quantification - C. virginica Gonad gDNA • kubu4 • November 14, 2017
• Assembly Comparison - Oly Assemblies Using Quast • kubu4 • November 14, 2017
• Genome Assembly - Olympia Oyster Illumina & PacBio Using PB Jelly w/BGI Scaffold Assembly • kubu4 • November 14, 2017
• Genome Assembly - Olympia Oyster Illumina & PacBio Using PB Jelly w/Platanus Assembly • kubu4 • November 14, 2017
• Samples Received - Tanner Crab Hemolymph in RNA Later from Pam Jensen • kubu4 • November 13, 2017
• RNA Isolation & Quantification - Tanner crab hemolymph • kubu4 • November 7, 2017

October 2017

• Software Installation - ALPACA on Roadrunner • kubu4 • October 31, 2017
• Software Crash - Olympia oyster genome assembly with Masurca on Mox • kubu4 • October 31, 2017
• Software Installation - PB Jelly Suite and Blasr on Emu • kubu4 • October 30, 2017
• Genome Assembly - Olympia oyster Illumina & PacBio Reads Using Redundans • kubu4 • October 24, 2017
• Assembly Comparison - Oly PacBio Canu: Sam vs. Sean with Quast • kubu4 • October 23, 2017
• FAIL - Missing Data on Owl! • kubu4 • October 23, 2017
• Genome Assembly - Olympia oyster Illumina & PacBio reads using MaSuRCA • kubu4 • October 19, 2017
• Software Installation - MaSuRCA v3.2.3 Assembler on Mox (Hyak) • kubu4 • October 19, 2017
• Fail - Directory Contents Deleted! • kubu4 • October 18, 2017
• Genome Assembly - Olympia oyster PacBio Canu v1.6 • kubu4 • October 18, 2017
• Data Management - Convert Oly PacBio H5 to FASTQ • kubu4 • October 9, 2017
• Genome Assembly - Olympia oyster Redundans/Canu vs. Redundans/Racon • kubu4 • October 6, 2017
• Genome Assembly - Olympia Oyster Redundans with Illumina + PacBio • kubu4 • October 5, 2017
• Genome Assembly - minimap/miniasm/racon Overview • kubu4 • October 4, 2017
• Assembly Comparisons - Olympia oyster genome assemblies • kubu4 • October 3, 2017
• Samples Received - C.virginica gonad tissue from Katie Lotterhos • kubu4 • October 3, 2017
• Goals - October 2017 • kubu4 • October 2, 2017

September 2017

• Genome Assembly - Olympia oyster PacBio minimap/miniasm/racon • kubu4 • September 18, 2017
• Genome Assembly - Olympia oyster PacBio minimap/miniasm/racon • kubu4 • September 18, 2017
• Genome Assembly - Olympia oyster PacBio minimap/miniasm/racon • kubu4 • September 7, 2017

August 2017

• Samples Submitted - Geoduck Ctenidia to Illumina for 10x Genomics Sequencing • kubu4 • August 28, 2017
• Project Progress - Olympia Oyster Genome Assemblies by Sean Bennett • kubu4 • August 28, 2017
• Data Management - Illumina Geoduck HiSeq & MiSeq Data • kubu4 • August 8, 2017
• Goals - August 2017 • kubu4 • August 3, 2017

July 2017

• Data Received - Geoduck Genome Sequencing by Illumina • kubu4 • July 31, 2017
• Sample Submission - Olympia oyster gonad RNA to Katherine Silliman @ Univ. of Chicago • kubu4 • July 20, 2017
• RNA Isolation - Olympia oyster gonad tissue in paraffin histology blocks • kubu4 • July 20, 2017
• RNA Isolation - Olympia oyster gonad tissue in paraffin histology blocks • kubu4 • July 10, 2017
• Data Management - SRA Submission Olympia Oyster UW PacBio Data from 20170323 • kubu4 • July 6, 2017
• Data Management – Tarball of Olympia oyster UW PacBio Data from 20170323 • kubu4 • July 6, 2017
• Data Management - OLYMPIA OYSTER UW PACBIO DATA (FROM 20170323) TO NIGHTINGALES • kubu4 • July 5, 2017
• Sample Annotation - Olympia oyster histology blocks (from Laura Spencer) • kubu4 • July 5, 2017
• Manuscript Re-submission - Oly Stress Response to PeerJ for Review • kubu4 • July 3, 2017
• Data Management - Olympia oyster UW PacBio Data from 20170323 • kubu4 • July 3, 2017

June 2017

• GitHub Curation • kubu4 • June 22, 2017
• Goals - June 2017 • kubu4 • June 1, 2017

May 2017

• DNA Methylation Quantification - Acropora cervicornis (Staghorn coral) DNA from Javier Casariego (FIU) • kubu4 • May 12, 2017
• DNA Quantification - Acropora cervicornis (Staghorn coral) DNA from Javier Casariego (FIU) • kubu4 • May 11, 2017
• DNA Concentration - Acropora cervicornis (Staghorn coral) DNA from Javier Casariego (FIU) • kubu4 • May 10, 2017
• DNA Quantification - Acropora cervicornis (Staghorn coral) DNA from Javier Casariego (FIU) • kubu4 • May 10, 2017
• Samples Received - Olympia oyster Histology Blocks and Slides (for Laura Spencer) • kubu4 • May 9, 2017
• Samples Received - Acropora cervicornis (Staghorn coral) DNA from Javier Casariego (FIU) • kubu4 • May 9, 2017
• Goals - May 2017 • kubu4 • May 3, 2017

April 2017

• Manuscript Writing - Submitted! • kubu4 • April 19, 2017
• Manuscript - Oly GBS 14 Day Plan • kubu4 • April 18, 2017

March 2017

• Data Received - Olympia oyster PacBio Data • kubu4 • March 23, 2017
• Data Management – SRA Submission Oly GBS Batch Submission • kubu4 • March 21, 2017
• Computing - Owl Partially Restored • kubu4 • March 21, 2017
• Data Management - SRA Submission Oly GBS Batch Submission Fail • kubu4 • March 20, 2017
• Troubleshooting - Synology NAS (Owl) Down After Update • kubu4 • March 18, 2017
• Computing – Oly BGI GBS Reproducibility; fail? • kubu4 • March 17, 2017
• Computing – Oly BGI GBS Reproducibility Fail (but, less so than last time)... • kubu4 • March 14, 2017
• Computing - Oly BGI GBS Reproducibility Fail • kubu4 • March 7, 2017
• FASTQC - Oly BGI GBS Raw Illumina Data Demultiplexed • kubu4 • March 7, 2017
• FASTQC - Oly BGI GBS Raw Illumina Data • kubu4 • March 3, 2017
• Goals - March 2017 • kubu4 • March 2, 2017

February 2017

• Manuscript Writing - More "Nuances" Using Authorea • kubu4 • February 28, 2017
• Data Received - Jay's Coral RADseq and Hollie's Geoduck Epi-RADseq • kubu4 • February 28, 2017
• Data Management - SRA Submission of Ostrea lurida GBS FASTQ Files • kubu4 • February 8, 2017
• Goals - February 2017 • kubu4 • February 2, 2017

January 2017

• Manuscript Writing - The "Nuances" of Using Authorea • kubu4 • January 23, 2017
• Sample Submission – Geoduck gDNA for Illumina Pilot Sequencing Project • kubu4 • January 5, 2017
• DNA Isolation - Geoduck gDNA for Illumina-initiated Sequencing Project • kubu4 • January 5, 2017
• Data Management - Replacement of Corrupt BGI Oly Genome FASTQ Files • kubu4 • January 4, 2017
• Goals - January 2017 • kubu4 • January 3, 2017

2016

</ul>

December 2016

• Data Management - Geoduck RRBS Data Integrity Verification • kubu4 • December 30, 2016
• Data Received - Geoduck RRBS Sequencing Data • kubu4 • December 30, 2016
• Sample Submission - Geoduck Tissue & gDNA for Illumina Pilot Sequencing Project • kubu4 • December 21, 2016
• DNA Isolation - Geoduck gDNA for Potential Illumina-initiated Sequencing Project • kubu4 • December 21, 2016
• Sample Submission - Geoduck Reduced Representation Bisulfite Pooled Libraries • kubu4 • December 20, 2016
• Sample Submission - Ostrea lurida gDNA for PacBio Sequencing • kubu4 • December 19, 2016
• Data Management - Integrity Check of Final BGI Olympia Oyster & Geoduck Data • kubu4 • December 15, 2016
• DNA Isolation - Ostrea lurida DNA for PacBio Sequencing • kubu4 • December 15, 2016
• Data Managment - Trim Output Cells from Jupyter Notebook • kubu4 • December 14, 2016
• Data Management - Download Final BGI Genome & Assembly Files • kubu4 • December 14, 2016
• Goals - December 2016 • kubu4 • December 2, 2016
• Data Analysis - Continued O.lurida Fst Analysis from GBS Data • kubu4 • December 2, 2016
• Computing - An Excercise in Futility • kubu4 • December 1, 2016

November 2016

• Data Analysis - Initial O.lurida Fst Determination from GBS Data • kubu4 • November 18, 2016
• Data Management - Tracking O.lurida FASTQ File Corruption • kubu4 • November 17, 2016
• Computer Management - Additional Configurations for Reformatted Xserves • kubu4 • November 16, 2016
• Data Management - Modify Eagle/Owl Cloud Sync Account • kubu4 • November 7, 2016
• Computing - Retrieve data from Amazon EC2 Instance • kubu4 • November 4, 2016
• Goals - November 2016 • kubu4 • November 2, 2016

October 2016

• Data Management – Geoduck Small Insert Library Genome Assembly from BGI • kubu4 • October 25, 2016
• Goals - October 2016 • kubu4 • October 3, 2016

September 2016

• Data Received – Jay’s Coral epiRADseq - Not Demultiplexed • kubu4 • September 19, 2016
• Oyster Sampling - Olympia Oyster OA Populations at Manchester • kubu4 • September 12, 2016
• Data Received - Jay's Coral epiRADseq • kubu4 • September 8, 2016
• Goals - September 2016 • kubu4 • September 6, 2016

August 2016

• Data Management - Synology Cloud Sync to UW Google Drive • kubu4 • August 29, 2016
• Server HDD Failure – Owl • kubu4 • August 22, 2016
• Manuscript Submission - Oly Stress Response to PeerJ for Review • kubu4 • August 18, 2016
• Data Analysis - fastStructure Population Analysis of Oly GBS PyRAD Output • kubu4 • August 17, 2016
• Computing - Amazon EC2 Cost "Analysis" • kubu4 • August 1, 2016
• Goals - August 2016 • kubu4 • August 1, 2016

July 2016

• Data Analysis - PyRad Analysis of Olympia Oyster GBS Data • kubu4 • July 27, 2016
• Computing - Not Enough Power! • kubu4 • July 18, 2016
• Computing - Amazon EC2 Instance Out of Space? • kubu4 • July 17, 2016
• Computing - A Very Quick "Guide" to Amazon EC2 Continued • kubu4 • July 14, 2016
• Dissection - Frozen Geoduck & Pacific Oyster • kubu4 • July 14, 2016
• Filter Replacement - Xserve Server Rack Enclosure • kubu4 • July 14, 2016
• Computing - The Very Quick "Guide" to Amazon Web Services Cloud Computing Instances (EC2) • kubu4 • July 13, 2016
• DNA Methylation Quantification - Coral DNA from Jose M. Eirin-Lopez (Florida International University) • kubu4 • July 8, 2016
• Goals - July 2016 • kubu4 • July 1, 2016

June 2016

• DNA Quantification - Coral DNA from Jose M. Eirin-Lopez (Florida International University) • kubu4 • June 30, 2016
• Samples Received - Coral DNA from Jose M. Eirin-Lopez (Florida International University) • kubu4 • June 15, 2016
• Docker - VirtualBox Defaults on OS X • kubu4 • June 14, 2016
• Docker - One liner to create Docker container • kubu4 • June 9, 2016
• RAM Upgrade - Roadrunner (Apple Xserve) to 48GB RAM • kubu4 • June 9, 2016
• Goals - June 2016 • kubu4 • June 6, 2016
• Docker - Improving Roberts Lab Reproducibility • kubu4 • June 1, 2016

May 2016

• Computer Setup - Cluster Node003 Conversion • kubu4 • May 31, 2016
• Data Analysis - Oly GBS Data Using Stacks 1.37 • kubu4 • May 23, 2016
• Data Management - Olympia Oyster Small Insert Library Genome Assembly from BGI • kubu4 • May 16, 2016
• GBS Frustrations • kubu4 • May 3, 2016
• Goals - May 2016 • kubu4 • May 2, 2016

April 2016

• SRA Release - Transcriptomic Profiles of Adult Female & Male Gonads in Panopea generosa (Pacific geoduck) • kubu4 • April 28, 2016
• Data Management - O.lurida Raw BGI GBS FASTQ Data • kubu4 • April 28, 2016
• Computing - Speed Benchmark Comparisons Between Local, External, & Server Files • kubu4 • April 27, 2016
• Data Analysis - Subset Olympia Oyster GBS Data from BGI as Single Population Using PyRAD • kubu4 • April 18, 2016
• Data Management - Concatenate FASTQ files from Oly MBDseq Project • kubu4 • April 11, 2016
• Data Analysis - Oly GBS Data from BGI Using Stacks • kubu4 • April 6, 2016
• Software Install - samtools-0.1.19 and stacks-1.37 • kubu4 • April 6, 2016

March 2016

• SRA Submission – Genome sequencing of the Olympia oyster (Ostrea lurida) • kubu4 • March 28, 2016
• SRA Submission – Genome sequencing of the Pacific geoduck (Panopea generosa) • kubu4 • March 28, 2016
• SRA Submission - Transcriptomic Profiles of Adult Female & Male Gonads in Panopea generosa (Pacific geoduck). • kubu4 • March 24, 2016
• SRA Submission - Individual Transcriptomic Profiles of C.gigas Before & After Heat Shock • kubu4 • March 23, 2016
• Data Management - SRA Submission Overview • kubu4 • March 23, 2016
• Data Management - O. lurida genotype-by-sequencing (GBS) data from BGI • kubu4 • March 15, 2016
• Data Received - Initial Geoduck Genome Assembly from BGI • kubu4 • March 14, 2016
• Data Received - Initial Olympia oyster Genome Assembly from BGI • kubu4 • March 14, 2016
• Data Management - O.lurida 2bRAD Dec2015 Undetermined FASTQ files • kubu4 • March 8, 2016

February 2016

• Data Management - High-throughput Sequencing Data • kubu4 • February 5, 2016
• Data Received - Ostrea lurida MBD-enriched BS-seq • kubu4 • February 3, 2016

January 2016

• Data Received - Ostrea lurida genome sequencing files from BGI • kubu4 • January 28, 2016
• Data Received - Panopea generosa genome sequencing files from BGI • kubu4 • January 28, 2016
• Data Analysis - Identification of duplicate files on Eagle • kubu4 • January 14, 2016
• Data Received - Bisulfite-treated Illumina Sequencing from Genewiz • kubu4 • January 9, 2016

2015

</ul>

December 2015

• Data Received - Oly 2bRAD Illumina Sequencing from Genewiz • kubu4 • December 31, 2015
• Sample Submission - BS-seq Library Pool to Genewiz • kubu4 • December 22, 2015
• Illumina Methylation Library Quantification - BS-seq Oly/C.gigas Libraries • kubu4 • December 22, 2015
• Illumina Methylation Library Construction - Oly/C.gigas Bisulfite-treated DNA • kubu4 • December 22, 2015
• Bioanalyzer - Bisulfite-treated Oly/C.gigas DNA • kubu4 • December 19, 2015
• Reagent Prep - RNA Pico 6000 Ladder • kubu4 • December 19, 2015
• Bisulfite Treatment - Oly Reciprocal Transplant DNA & C.gigas Lotterhos DNA for BS-seq • kubu4 • December 18, 2015
• Agarose Gel - Oly gDNA for BS-seq Libraries, Take Two • kubu4 • December 18, 2015
• Agarose Gel - Oly gDNA for BS-seq Libraries • kubu4 • December 17, 2015
• DNA Isolation - Oly gDNA for BS-seq • kubu4 • December 17, 2015
• Sample Submission - 2bRAD Libraries for Genewiz • kubu4 • December 10, 2015
• Samples Received - C.gigas Tissue & DNA from Katie Lotterhos • kubu4 • December 10, 2015
• Sample Submission - Olympia oyster MBD-enriched DNA to ZymoResearch • kubu4 • December 9, 2015
• Sample Submission - Additional Olympia Oyster gDNA for Genome Sequencing @ BGI • kubu4 • December 1, 2015
• Sample Submission - Additional Geoduck gDNA for Genome Sequencing @ BGI • kubu4 • December 1, 2015

November 2015

• Data Storage - Synology DX513 • kubu4 • November 30, 2015
• Sample Submission - Oly Oyster Bay Tissues for GBS • kubu4 • November 30, 2015
• Samples Received - Oly Tissue & DNA from Katherine Silliman • kubu4 • November 25, 2015
• DNA Quality Assessment - Geoduck & Olympia Oyster gDNA • kubu4 • November 25, 2015
• DNA Isolation - Olympia Oyster Outer Mantle gDNA • kubu4 • November 25, 2015
• DNA Isolation - Geoduck Ctenidia gDNA • kubu4 • November 25, 2015
• Phenol-Chloroform DNA Cleanup - Geoduck gDNA • kubu4 • November 25, 2015
• Phenol-Chloroform DNA Cleanup - Olympia Oyster gDNA • kubu4 • November 25, 2015
• DNA Isolation - Geoduck Adductor Muscle gDNA • kubu4 • November 25, 2015
• DNA Isolation - Olympia Oyster Outer Mantle gDNA • kubu4 • November 25, 2015
• DNA Quantification - MBD-enriched Olympia oyster DNA • kubu4 • November 23, 2015
• Ethanol Precipitation - Olympia oyster MBD • kubu4 • November 22, 2015
• MBD Enrichment - Sonicated Olympia Oyster gDNA • kubu4 • November 22, 2015
• DNA Sonication - Oly gDNA for MBD • kubu4 • November 20, 2015
• qPCR – Oly RAD-Seq Library Quantification • kubu4 • November 18, 2015
• qPCR - Oly RAD-Seq Library Quantification • kubu4 • November 17, 2015
• Gel Extraction - Oly RAD-Seq Prep Scale PCR • kubu4 • November 17, 2015
• DNA Quality Assessment - Geoduck, Oly & Oly 2SN • kubu4 • November 14, 2015
• PCR – Oly RAD-seq Prep Scale PCR • kubu4 • November 14, 2015
• PCR – Oly RAD-seq Test-scale PCR • kubu4 • November 13, 2015
• DNA Quantification & Quality Assessment - Oly 2SN gDNA • kubu4 • November 5, 2015
• DNA Quantification & Quality Assessment - Geoduck & Oly gDNA • kubu4 • November 5, 2015
• DNA Isolations – Oly Fidalgo 2SN Ctenidia • kubu4 • November 4, 2015

October 2015

• Oyster Sampling - Oly Fidalgo 2SN, 2HL, 2NF Reciprocal Transplants Final Samplings • kubu4 • October 31, 2015
• DNA Isolation – Geoduck & Olympia Oyster • kubu4 • October 30, 2015
• Adaptor Ligation – Oly AlfI-Digested gDNA for RAD-seq • kubu4 • October 30, 2015
• Restriction Digest – Oly gDNA for RAD-seq w/AlfI • kubu4 • October 29, 2015
• Troubleshooting - Oly RAD-seq • kubu4 • October 23, 2015
• DNA Isolations - Fidalgo 2SN Reciprocal Transplants Final Samplings • kubu4 • October 22, 2015
• PCR - Oly RAD-seq Prep Scale PCR • kubu4 • October 13, 2015
• PCR - Oly RAD-seq Test-scale PCR • kubu4 • October 12, 2015
• Adaptor Ligation – Oly AlfI-Digested gDNA for RAD-seq • kubu4 • October 9, 2015
• Restriction Digest – Oly gDNA for RAD-seq w/AlfI • kubu4 • October 9, 2015
• Sample Submission - Additional Geoduck gDNA for Genome Sequencing @ BGI • kubu4 • October 6, 2015
• Sample Submission - Additional Olympia Oyster gDNA for Genome Sequencing @ BGI • kubu4 • October 6, 2015
• Agarose Gel - Geoduck & Olympia Oyster gDNA • kubu4 • October 6, 2015
• DNA Quantification - Pooled geoduck gDNA • kubu4 • October 5, 2015
• gDNA Isolation - Geoduck Adductor Muscle • kubu4 • October 5, 2015
• DNA Isolation - Geoduck & Olympia Oyster • kubu4 • October 3, 2015
• PCR - Oly RAD-seq Test-scale PCR • kubu4 • October 2, 2015
• PCR - Oly RAD-seq Test-scale PCR • kubu4 • October 1, 2015
• Adaptor Ligation - Oly AlfI-Digested gDNA for RAD-seq • kubu4 • October 1, 2015
• Goals - October 2015 • kubu4 • October 1, 2015

September 2015

• Restriction Digest - Oly gDNA for RAD-seq w/AlfI • kubu4 • September 30, 2015
• Sample Submission - Olympia Oyster gDNA for Genome Sequencing @ BGI • kubu4 • September 21, 2015
• Sample Submission - Geoduck gDNA for Genome Sequencing @ BGI • kubu4 • September 21, 2015
• Uninterruptible Power Supplies (UPS) • kubu4 • September 19, 2015
• Agarose Gel - Geoduck & Olympia oyster gDNA Integrity Check • kubu4 • September 18, 2015
• Ethanol Precipitation - Geoduck & Olympia oyster gDNA • kubu4 • September 17, 2015
• Agarose Gel - Olympia oyster Whole Body gDNA Integrity Check • kubu4 • September 17, 2015
• DNA Isolation - Olympia oyster whole body • kubu4 • September 17, 2015
• Agarose Gel – Geoduck gDNA Integrity Check • kubu4 • September 16, 2015
• Genomic DNA Isolation – Geoduck Adductor Muscle & Foot • kubu4 • September 16, 2015
• Agarose Gel - Geoduck & Olympia Oyster gDNA Integrity Check • kubu4 • September 16, 2015
• Genomic DNA Isolation – Olympia oyster adductor musle & mantle • kubu4 • September 15, 2015
• Genomic DNA Isolation – Geoduck Adductor Muscle & Foot • kubu4 • September 15, 2015
• Agarose Gel - Geoduck & Olympia Oyster gDNA Integrity Check • kubu4 • September 15, 2015
• Genomic DNA Isolation - Olympia oyster adductor musle & mantle • kubu4 • September 15, 2015
• Genomic DNA Isolation - Geoduck Adductor Muscle & Foot • kubu4 • September 15, 2015
• Agarose Gel - Geoduck & Olympia Oyster gDNA Integrity Check • kubu4 • September 2, 2015
• Genomic DNA Isolation - Olympia oyster adductor musle & mantle • kubu4 • September 2, 2015
• Server Email Notifications Fix - Eagle • kubu4 • September 1, 2015

August 2015

• Genomic DNA Isolation - Geoduck Adductor Muscle & Foot • kubu4 • August 29, 2015
• RAD-Seq Library Prep Reagents • kubu4 • August 19, 2015
• SsoFast EvaGreen Supermix Aliquots • kubu4 • August 11, 2015
• Reverse Transcription – O.lurida DNased RNA 1hr post-mechanical stress • kubu4 • August 6, 2015
• qPCR - Jake's O.lurida ctenidia 1hr post-mechanical stress DNased RNA • kubu4 • August 6, 2015
• RNA Quantification - O.lurida 1hr post-mechanical heat stress DNased RNA • kubu4 • August 6, 2015
• Goals - August 2015 • kubu4 • August 3, 2015

July 2015

• Sample Submission – Olympia oyster PCRs Sanger Sequencing • kubu4 • July 31, 2015
• Server HDD Failure - Owl • kubu4 • July 31, 2015
• DNase Treatment - O.lurida Ctenidia 1hr Post-Mechanical Stress RNA • kubu4 • July 27, 2015
• RNA Isolation – O.lurida Ctenidia 1hr Post-Mechanical Stress • kubu4 • July 16, 2015
• RNA Isolation - O.lurida Ctenidia 1hr Post-Mechanical Stress • kubu4 • July 11, 2015
• SsoFast EvaGreen Supermix Aliquots • kubu4 • July 10, 2015
• Automatic Notebook Backups - wget Script & Synology Task Scheduler • kubu4 • July 3, 2015
• PCR - Sea Pen luciferase • kubu4 • July 2, 2015
• GOALS - July 2015 • kubu4 • July 2, 2015
• Opticon2 Calibration • kubu4 • July 1, 2015

June 2015

• RNAseq Data Receipt - Geoduck Gonad RNA 100bp PE Illumina • kubu4 • June 30, 2015
• Sample Submission – Olympia oyster PCRs Sanger Sequencing • kubu4 • June 25, 2015
• Reverse Transcription - O.lurida DNased RNA Controls and 1hr Heat Shock • kubu4 • June 17, 2015
• Sample Submission – Olympia oyster & Sea Pen PCRs Sanger Sequencing • kubu4 • June 16, 2015
• Gel Purification - Olympia Oyster and Sea Pen PCRs • kubu4 • June 16, 2015
• Sample Submission - Olympia oyster PCRs Sanger Sequencing • kubu4 • June 12, 2015
• Sample Submission - Geoduck Gonad for RNA-seq • kubu4 • June 1, 2015
• Goals - June 2015 • kubu4 • June 1, 2015

May 2015

• Bioanalyzer - Geoduck Gonad RNA Quality Assessment • kubu4 • May 28, 2015
• Reverse Transcription - Subset of Jake's O.lurida DNased RNA • kubu4 • May 22, 2015
• Bioinformatics – Trimmomatic/FASTQC on C.gigas Larvae OA NGS Data • kubu4 • May 22, 2015
• qPCR - Re-run Jake's O.lurida DNased RNA Samples NC1, SC1, SC2, SC4 from 20150514 • kubu4 • May 22, 2015
• qPCR – Jake's O.lurida ctenidia DNased RNA (1hr Heat Shock Samples) • kubu4 • May 15, 2015
• qPCR – Jake's O.lurida ctenidia DNased RNA (Control Samples) • kubu4 • May 15, 2015
• DNase Treatment - Jake's O.lurida Ctenidia RNA (1hr Heat Shock) from 20150506 • kubu4 • May 15, 2015
• DNase Treatment - Jake's O.lurida Ctenidia RNA (Controls) from 20150507 • kubu4 • May 14, 2015
• ISO Creation - OpticonMonitor3 Disc Cloning • kubu4 • May 14, 2015
• qPCR - Jake O.lurida ctenidia RNA (Heat Shock Samples) from 20150506 • kubu4 • May 13, 2015
• qPCR - Jake O.lurida ctenidia RNA (Control Samples) From 20150507 • kubu4 • May 13, 2015
• RNA Isolation – Geoduck Gonad in Paraffin Histology Blocks • kubu4 • May 8, 2015
• RNA Isolation – Jake’s O. lurida Ctenidia Control from 20150422 • kubu4 • May 7, 2015
• Bioinformatics - Trimmomatic/FASTQC on C.gigas Larvae OA NGS Data • kubu4 • May 7, 2015
• RNA Isolation - Jake's O. lurida Ctenidia 1hr Heat Stress from 20150422 • kubu4 • May 7, 2015
• RNA Isolation – Geoduck Gonad in Paraffin Histology Blocks • kubu4 • May 5, 2015
• RNA Isolation – Geoduck Gonad in Paraffin Histology Blocks • kubu4 • May 5, 2015
• BLAST - C.gigas Larvae OA Illumina Data Against GenBank nt DB • kubu4 • May 4, 2015
• Goals - May 2015 • kubu4 • May 1, 2015

April 2015

• BLASTN - C.gigas OA Larvae to C.gigas Ensembl 1.24 BLAST DB • kubu4 • April 30, 2015
• RNA Isolation – Geoduck Gonad in Paraffin Histology Blocks • kubu4 • April 27, 2015
• Bioanalyzer Data - Geoduck RNA from Histology Blocks • kubu4 • April 24, 2015
• RNA Isolation – Geoduck Gonad in Paraffin Histology Blocks • kubu4 • April 24, 2015
• Bioanalyzer Submission - Geoduck Gonad RNA from Histology Blocks • kubu4 • April 22, 2015
• Quality Trimming - C.gigas Larvae OA BS-Seq Data • kubu4 • April 16, 2015
• Quality Trimming - LSU C.virginica Oil Spill MBD BS-Seq Data • kubu4 • April 16, 2015
• Sequence Data Analysis - LSU C.virginica Oil Spill MBD BS-Seq Data • kubu4 • April 14, 2015
• Sequence Data Analysis - C.gigas Larvae OA BS-Seq Data • kubu4 • April 14, 2015
• Sequence Data - C.gigas OA Larvae BS-Seq Demultiplexed • kubu4 • April 13, 2015
• Sequence Data - LSU C.virginica Oil Spill MBD BS-Seq Demultiplexed • kubu4 • April 13, 2015
• RNA Isolation - Geoduck Gonad in Paraffin Histology Blocks • kubu4 • April 9, 2015

March 2015

• Sequencing Data - C.gigas Larvae OA • kubu4 • March 20, 2015
• Epinext Adaptor 1 Counts - LSU C.virginica Oil Spill Samples • kubu4 • March 17, 2015
• TruSeq Adaptor Counts – LSU C.virginica Oil Spill Sequences • kubu4 • March 16, 2015
• TruSeq Adaptor Identification Method Comparison - LSU C.virginica Oil Spill Sequences • kubu4 • March 14, 2015
• DNA Quantification - Claire's C.gigas Sheared DNA • kubu4 • March 4, 2015
• Library Quality Assessment - C.gigas OA larvae Illumina libraries • kubu4 • March 2, 2015

February 2015

• BS-seq Library Prep - C.gigas Larvae OA 1000ppm • kubu4 • February 28, 2015
• DNA Quantification - C.gigas Larvae 1000ppm • kubu4 • February 27, 2015
• DNA Quantification - Claire's Sheared C.gigas Mantle Heat Shock Samples • kubu4 • February 27, 2015
• Bioanalyzer - C.gigas Sheared DNA from 20140108 • kubu4 • February 20, 2015
• Library Prep - Quantification of C.gigas larvae OA 1000ppm library • kubu4 • February 9, 2015
• Sequencing Data - LSU C.virginica MBD BS-Seq • kubu4 • February 9, 2015
• Bisulfite NGS Library Prep - Bisulfite Conversion & Illumina Library Construction of C.gigas larvae DNA • kubu4 • February 7, 2015

January 2015

• Bisuflite NGS Library Prep – C.gigas larvae OA bisulfite library quantification • kubu4 • January 28, 2015
• Bisuflite NGS Library Prep - C.gigas larvae OA bisulfite DNA (continued from yesterday) • kubu4 • January 28, 2015
• Bisuflite NGS Library Prep - C.gigas larvae OA bisulfite DNA • kubu4 • January 27, 2015
• Library Cleanup - LSU C.virginica MBD BS Library • kubu4 • January 23, 2015
• DNA Bisulfite Conversion - C.gigas larvae OA Sheared DNA • kubu4 • January 15, 2015
• SpeedVac - C.gigas larvae OA DNA • kubu4 • January 13, 2015
• DNA Isolation - C.gigas larvae from 2011 NOAA OA Experiment • kubu4 • January 9, 2015

2014

</ul>

December 2014

• Bisulfite NGS Library - LSU C.virginica Oil Spill MBD Bisulfite DNA Sequencing Submission • kubu4 • December 23, 2014
• Bisulfite NGS Library Prep - LSU C.virginica Oil Spill MBD Bisulfite DNA and Emma's C.gigas Larvae OA Bisulfite DNA (continued from yesterday) • kubu4 • December 19, 2014
• Bisulfite NGS Library Prep - LSU C.virginica Oil Spill Bisulfite DNA and Emma's C.gigas Larvae OA Bisulfite DNA • kubu4 • December 18, 2014
• Bisulfite Conversion - LSU C.virginica Oil Spill MBD DNA and Emma's C.gigas Larvae OA DNA • kubu4 • December 17, 2014
• DNA Isolation - Claire's C.gigas Female Gonad for Illumina Bisulfite Sequencing • kubu4 • December 11, 2014
• EtOH Precipitation - LSU C.virginica Oil Spill MBD Continued (from 20141126) • kubu4 • December 3, 2014

November 2014

• Methylated DNA Enrichment (MBD) - LSU C.virginica Oil Spill gDNA • kubu4 • November 27, 2014
• Gel - Sheared LSU C.virginica Oil Spill gDNA (from yesterday) • kubu4 • November 27, 2014
• DNA Shearing - LSU C.virginica Oil Spill gDNA • kubu4 • November 26, 2014
• Gel - Sheared gDNA • kubu4 • November 26, 2014
• RNA Seq - C.gigas Total RNA from Claire's Pre/Post Heat Shock • kubu4 • November 24, 2014
• DNA Isolation - C.gigas Larvae from Emma OA Experiments • kubu4 • November 21, 2014
• RAD Sequencing - Oly Oyster gDNA-01 RAD Library (from 20141110) • kubu4 • November 17, 2014
• DNA Quantification - Oly Oyster gDNA-01 RAD Library • kubu4 • November 10, 2014
• Library Prep - Oly Oyster gDNA-01 RAD • kubu4 • November 7, 2014
• DNA Shearing & Size Selection - Oly Oyster gDNA RAD P1 Adapters (from 20141105) • kubu4 • November 6, 2014
• Ligation - Illumina P1 Adapters for Oly Oyster gDNA-01 RAD Sequencing (from 20141031) • kubu4 • November 5, 2014

October 2014

• Restriction Digest - Oly Oyster gDNA-01 for RAD Sequencing (from 20141029) • kubu4 • October 31, 2014
• DNA Allocation - Oly Oyster gDNA-01 for RAD Sequencing (from 20141022) • kubu4 • October 30, 2014
• DNA Quantification - Oly Oyster gDNA-01 for RAD Sequencing (from 20141014) • kubu4 • October 23, 2014
• DNA Isolation - Olympia Oyster Populations for RAD Sequencing • kubu4 • October 15, 2014

September 2014

• Package - Received Package from Jerome LaPeyre from LSU • kubu4 • September 27, 2014
• DNA Isolation - C.gigas Larvae from Katie Latterhos • kubu4 • September 24, 2014
• DNA Isolation - C.gigas Larvae from Katie Latterhos and Emma • kubu4 • September 23, 2014
• PCR - Mac's Bisulfite-Treated DNA • kubu4 • September 4, 2014

August 2014

• PCR - Mac's Bisulfite-Treated DNA • kubu4 • August 29, 2014

May 2014

• RNA-Seq - Sea Star Data Download • kubu4 • May 29, 2014
• RNA Isolation - Jessica's Geoduck Larval Stages • kubu4 • May 27, 2014
• DNA Isolation - Mackenzie's C.gigas EE2 Gonad Samples • kubu4 • May 16, 2014
• Sample Submission - Colleen Sea Star (Pycnopodia) Coelomycete RNA for Illumina Sequencing • kubu4 • May 14, 2014
• RNA Isolation - Colleen Sea Star (Pycnopodia) Coelomycete Sample • kubu4 • May 8, 2014

April 2014

• RNA Isolation - Colleen Sea Star (Pycnopodia) Coelomycete Samples • kubu4 • April 28, 2014
• DNA Isolation - Claire's C.gigas Female Gonad • kubu4 • April 25, 2014
• Ethanol Precipitation - Colleen's Sea Star Coelomycete RNA from Yesterday • kubu4 • April 25, 2014
• RNA Clean Up - Colleen's Sea Star Coelomycete RNA from 20140416 • kubu4 • April 24, 2014
• RNA Isolation - Colleens' Sea Star Coelomycetes Samples • kubu4 • April 16, 2014
• DNA Isolation - Test Sample • kubu4 • April 16, 2014
• Phenol-Chloroform DNA Clean Up - Mac and Claire's Samples (from 20140410) • kubu4 • April 14, 2014
• RNA Isolation - Sea Star Coelomocytes (from Colleen) • kubu4 • April 10, 2014
• DNA Isolation - Claire's C.gigas Female Gonad and Mac's C.gigas Gonad • kubu4 • April 10, 2014
• Cloned Hard Drive - Windows XP Opticon Computer (Aquacul8) • kubu4 • April 4, 2014
• DNA gel - Claire's C.gigas Female Gonad and Mac's C.gigas Gonad • kubu4 • April 4, 2014
• RNA Isolation - Sea Star Coelomocytes (provided by Colleen Burge) • kubu4 • April 2, 2014
• RNA Isolation - Sea Star Coelomocytes (provided by Colleen Burge) • kubu4 • April 1, 2014
• DNA Isolation - Mackenzie's C.gigas Gonad Sample • kubu4 • April 1, 2014

March 2014

• DNA Isolation - C.gigas Female Gonads (from frozen) • kubu4 • March 28, 2014
• DNA Quality Check - Yanouk's Oyster gDNA • kubu4 • March 14, 2014

February 2014

• DNA Isolation - Geoduck • kubu4 • February 19, 2014
• DNA Precipitation - Geoduck DNA from 20140213 • kubu4 • February 18, 2014
• DNA Isolation - Geoduck • kubu4 • February 13, 2014
• DNA Isolation - Geoduck • kubu4 • February 12, 2014

2013

</ul>

December 2013

• Gylcogen Assay - Emma's C.gigas Whole Body Samples (continued from yesterday) • kubu4 • December 7, 2013
• Gylcogen Assay - Emma's C.gigas Whole Body Samples • kubu4 • December 6, 2013

November 2013

• Gylcogen & Carboyhydrate Assays - Emma's C.gigas Whole Body Samples (continued from yesterday) • kubu4 • November 26, 2013
• Gylcogen and Carboyhydrate Assays - Emma's C.gigas Whole Body Samples • kubu4 • November 25, 2013

October 2013

• PCR - Lake Trout C1q • kubu4 • October 28, 2013
• PCR - Lake Trout C1q • kubu4 • October 10, 2013
• DNA Quantification - Yanouk's DNA Samples • kubu4 • October 4, 2013

September 2013

• PCR - Lake Trout C1q • kubu4 • September 19, 2013

April 2013

• PCR - Hexokinase Partial CDS • kubu4 • April 9, 2013
• PCR - Hexokinase and Partial Exon #1 • kubu4 • April 8, 2013

March 2013

• PCR - Hexokinase Promoter and CDS (repeat from 20130227) • kubu4 • March 14, 2013

February 2013

• PCR - Hexokinase Promoter and CDS • kubu4 • February 27, 2013
• Reverse Transcription - Herring RNA from 20091026 • kubu4 • February 13, 2013

2012

</ul>

November 2012

• qPCR - Halley cDNA Check • kubu4 • November 28, 2012
• Reverse Transcription - FISH441 RNA • kubu4 • November 21, 2012
• qPCR - Manila Clam Larvae cDNA (from August 2012 - Dave's Notebook) • kubu4 • November 9, 2012
• qPCR - Manila Clam Larvae cDNA (from August 2012 - Dave's Notebook) • kubu4 • November 9, 2012
• qPCR - Manila Clam Larvae cDNA (from August 2012 - Dave's Notebook) • kubu4 • November 8, 2012

October 2012

• qPCR - DNased Manila Clam Larvae RNA (from August 2012 - Dave's Notebook) • kubu4 • October 26, 2012
• Received oysters from Taylor Shellfish. • kubu4 • October 16, 2012
• qPCR - Opticon Test • kubu4 • October 10, 2012

July 2012

• Minipreps - Emma's Illumina Library Cloning • kubu4 • July 23, 2012
• Illumina RNAseq Library Construction - 32 C.gigas Individuals • kubu4 • July 11, 2012
• Oligo Reconstitution - Illumina RNAseq Library Oligos and Barcodes • kubu4 • July 11, 2012
• Chloroform Clean Up - Lexie's QPX RNA from 20110504 • kubu4 • July 10, 2012
• Sample Submission - QPX RNA and DNA for Illumina 36bp single-end RNA/DNAseq • kubu4 • July 9, 2012
• QPX Sample Pooling for Illumina Sequencing • kubu4 • July 6, 2012

May 2012

• qPCR - Detection of V.tubiashii Presence and Expression Using VtpA Primers in DNA/cDNA from yesterday • kubu4 • May 1, 2012

April 2012

• Reverse Transcription - DNased C.gigas Larval RNA from 20120427 • kubu4 • April 30, 2012
• qPCR - Check DNased RNA from Earlier Today for Residual gDNA • kubu4 • April 28, 2012
• DNase Treatment - C.gigas Larvae RNA from yesterday • kubu4 • April 28, 2012
• gDNA Isolation - C.gigas Larvae from Taylor Summer 2011 • kubu4 • April 27, 2012
• RNA Isolation - C.gigas Larvae from Taylor Summer 2011 • kubu4 • April 27, 2012

March 2012

• qPCR - Taylor Water Filter DNA Extracts from 20120322 • Sam White • March 27, 2012
• qPCR - Repeat of qPCR from Earlier Today • kubu4 • March 24, 2012
• qPCR - Taylor Water Filter DNA Extracts from Yesterday • kubu4 • March 24, 2012
• DNA Extraction - Taylor Water Filter Samples from 2011 • kubu4 • March 23, 2012
• Reverse Transcription - Dave's Manila Clam (Venerupis philippinarum) DNased RNA from 20120307 and 20120302 • kubu4 • March 13, 2012
• qPCR - Dave's Manila Calm (Venerupis philippinarum) DNased RNA from yesterday and 20120302 • kubu4 • March 9, 2012
• RNA Isolation - Dave's Manila Clam (Venerupis philippinarum) Gill Samples (#25-48) • kubu4 • March 8, 2012
• DNase - Dave's Manila Clam (Venerupis philippinarum) Gill RNA from Yesterday • kubu4 • March 3, 2012
• RNA Isolation - Dave's Manila Clam (Venerupis philippinarum) Gill Samples (#1-24) • kubu4 • March 2, 2012

February 2012

• qPCR - cDNA from 20120208 • kubu4 • February 10, 2012
• qPCR - cDNA from earlier today • kubu4 • February 9, 2012
• Reverse Transcription - C.gigas larvae DNased RNA (from 20120125) • kubu4 • February 9, 2012

January 2012

• qPCR - DNased RNA from earlier today • kubu4 • January 26, 2012
• DNAse - C.gigas RNA from 20120124 • kubu4 • January 26, 2012
• RNA Isolation - C.gigas Larvae from 20110412 & 20110705 (Continued from 20120112) • kubu4 • January 25, 2012
• RNA Isolation - C.gigas Larvae from 20110412 & 20110705 • kubu4 • January 13, 2012

2011

</ul>

October 2011

• Sequencing - COX/PGS Clones from yesterday/today • kubu4 • October 15, 2011
• Mini-preps - COX/PGS Cloning Colonies from today • kubu4 • October 14, 2011
• PCR - COX/PGS Cloning Colony Screens from yesterday • kubu4 • October 14, 2011
• Cloning - Purified COX/PGS "qPCR Fragment" from 20111006 • kubu4 • October 13, 2011
• PCR - Purified COX/PGS 1/2 DNA from earlier today • kubu4 • October 7, 2011
• PCR - Region Outside of COX/PGS qPCR Primers • kubu4 • October 7, 2011

September 2011

• Ethanol Precipitation - Full-length PGS1 cDNA (from 20110921) • kubu4 • September 30, 2011
• PCR - Full-length PGS1 cDNA • kubu4 • September 22, 2011
• Ethanol Precipitation - Purified PGS1 PCR from yesterday • kubu4 • September 22, 2011
• PCR - Full-length PGS1 cDNA • kubu4 • September 21, 2011
• PCR - Full-length PGS2 cDNA • kubu4 • September 15, 2011

August 2011

• PCR - Full-length PGS1 & PGS2 cDNAs • kubu4 • August 26, 2011
• qPCR - C.gigas V.vulnificus Exposure cDNA (from 20110311) • kubu4 • August 12, 2011
• Sequencing - C.gigas COX2/PGS2 Clone #4 from 20110728 • kubu4 • August 5, 2011

July 2011

• Plasmid Isolation & Sequencing - C.gigas COX2/PGS2 Clones (from yesterday) • kubu4 • July 29, 2011
• Bacterial Cultures - C.gigas COX2/PGS2 Clones (from yesterday) • kubu4 • July 28, 2011
• Colony PCRs - C.gigas COX2/PGS2 Clones (from yesterday) • kubu4 • July 27, 2011
• Cloning - C.gigas COX2/PGS2 5'/3' RACE Products (from earlier today) • kubu4 • July 26, 2011
• 5'/3' RACE - C.gigas COX2/PGS2 Nested RACE PCR • kubu4 • July 26, 2011
• 5'/3' RACE - C.gigas COX2/PGS2 RACE PCR • kubu4 • July 23, 2011
• Sequencing - PGS Hi 4 (PGS2/COX2) • kubu4 • July 16, 2011
• Plasmid Isolation - Miniprep on PGS Hi 4 Colony from yesterday • kubu4 • July 13, 2011
• PCR - Colony PCR on Restreaked PGS2 Clones from 20110707 • kubu4 • July 12, 2011
• Bacterial Cultures - Liquid Cultures of PGS2/COX2 Colonies from 20110707 • kubu4 • July 12, 2011
• Clone Restreaking - PGS2 Hi/Lo Clones (from 20110421) • kubu4 • July 8, 2011

June 2011

• qPCR - C.gigas GAPDH second rep on V.vulnificus exposure cDNA (from 20110311) and standard curves for COX1, COX2, GAPDH • kubu4 • June 4, 2011
• qPCR - C.gigas actin and GAPDH on V.vulnificus exposure cDNA (from 20110311) • kubu4 • June 3, 2011
• qPCR - C.gigas 18s and EF1a on V.vulnificus exposure cDNA (from 20110311) • kubu4 • June 3, 2011
• qPCR - C.gigas COX2 on V.vulnificus exposure cDNA (from 20110311) • kubu4 • June 1, 2011
• qPCR - C.gigas COX1 on V.vulnificus exposure cDNA (from 20110311) • kubu4 • June 1, 2011

May 2011

• qPCR - Hard Clam NGS Primer Checks • kubu4 • May 23, 2011
• qPCR - Lexie's QPX Temp & Tissue Experiment (see Lexies Notebook 4/26/2011) • kubu4 • May 20, 2011
• qPCR - Emma's New 3KDSqPCR Primers • kubu4 • May 20, 2011
• Reverse Transcription - Hard Clam Gill DNased RNA (from 20110509) • kubu4 • May 11, 2011
• DNase - Hard Clam Gill RNA (from earlier today) • kubu4 • May 9, 2011
• RNA Isolation - Hard Clam Gill Tissue from Vibrio Experiment (see Dave's Notebook 5/2/2011) • kubu4 • May 9, 2011
• Primer Design - Hard Clam NGS Primers • kubu4 • May 8, 2011
• RNA Isolation - Hard Clam Gill Tissue from Vibrio Experiment (see Dave's Notebook 5/2/2011) • kubu4 • May 6, 2011

April 2011

• Received - Live Hard Clams From Scott Lindell • kubu4 • April 28, 2011
• Bacterial Cultures - Colonies Selected from Yesterday's Colony PCRs • kubu4 • April 26, 2011
• Mini Preps - Liquid Cultures from yesterday • kubu4 • April 26, 2011
• Bacterial Cultures - Colonies Selected by Steven from Steven's Re-Streaked Plate • kubu4 • April 25, 2011
• Colony PCR - Colonies from COX1 Genomic Cloning (from 20110411) • kubu4 • April 25, 2011
• Colony PCR - 5'RACE Colony: COX2 (repeat of yesterday's PCR) • kubu4 • April 22, 2011
• Colony PCR - 5' RACE Colony: COX2 • kubu4 • April 21, 2011
• Colony PCR - 5' RACE Colonies • kubu4 • April 14, 2011
• Ligations - COX1/COX2 PCR Products • kubu4 • April 11, 2011
• 5'/3' RACE PCRs - Nested PCRs for COX2 Sequence • kubu4 • April 7, 2011
• 5'/3' RACE PCRs - COX2 Sequence on 5' & 3' RACE Libraries (from 20080619) • kubu4 • April 6, 2011

March 2011

• qPCR - C.gigas BB/DH cDNA for PROPS (TIMP3(BB) primers) • kubu4 • March 21, 2011
• qPCR - C.gigas BB/DH cDNA for PROPS (HMGP primers) • kubu4 • March 21, 2011
• qPCR - C.gigas COX1/COX2 Tissue Distribution • kubu4 • March 15, 2011
• qPCR - C.gigas BB/DH cDNA for PROPS • kubu4 • March 14, 2011
• Reverse Transcription - C.gigas BB/DH DNased RNA (from 20090507) for PROPS • kubu4 • March 11, 2011
• Reverse Transcription - C.gigas DNased RNA (from 20110131) from V.vulnificus Exposure & Tissues (from 20110111) • kubu4 • March 11, 2011
• SOLiD Sequencing Submission • kubu4 • March 10, 2011
• mRNA Isolation - Pooled Black Abalone Dg RNA (from Abalone Dg Exp 1) • kubu4 • March 7, 2011
• 3'RACE - C.gigas 3'RACE for COX2 • kubu4 • March 4, 2011
• NanoDrop1000 Comparison - Roberts vs. Young Lab • kubu4 • March 1, 2011
• qPCR - Check DNased RNA BB01 for Residual gDNA (from earlier today) • kubu4 • March 1, 2011
• DNase - C.gigas BB01 (PROPS) RNA (from 20090507) • kubu4 • March 1, 2011

February 2011

• qPCR - Check DNased RNA BB01 for Residual gDNA (from earlier today) • kubu4 • February 28, 2011
• DNase - C.gigas BB01 from 20110225 • kubu4 • February 28, 2011
• Ethanol Precpitation - DNased RNA BB01 (from earlier today) • kubu4 • February 25, 2011
• qPCR - Check DNased RNA BB01 for Residual gDNA (from earlier today) • kubu4 • February 25, 2011
• DNase - C.gigas BB01 from 20110216 • kubu4 • February 25, 2011
• Ethanol Precipitation - DNased RNA BB01 (from earlier today) • kubu4 • February 17, 2011
• qPCR - Check DNased RNA BB01 & 09 (from earlier today) • kubu4 • February 17, 2011
• DNase - C.gigas BB/DH (PROPS) RNA (from 20090507) • kubu4 • February 17, 2011
• Data Analysis - Young Lab ABI 7300 Calibration Checks • kubu4 • February 10, 2011
• qPCR - Test Young Lab qPCR Calibration • kubu4 • February 10, 2011
• NanoDrop1000 Comparison - Roberts vs. Young Lab • kubu4 • February 10, 2011
• qPCR - Test Young Lab qPCR Calibration (Repeat) • kubu4 • February 9, 2011
• PCR - New C. gigas COX Primers for Sequencing of Isoforms • kubu4 • February 9, 2011
• qPCR - Test Young Lab qPCR Calibration (Repeat) • kubu4 • February 9, 2011
• qPCR - Test Young Lab qPCR Calibration (Repeat) • kubu4 • February 5, 2011
• qPCR - Test Young Lab qPCR Calibration • kubu4 • February 5, 2011
• Genomic PCR - Repeat of C.gigas COX genomic PCR from 20110118 • kubu4 • February 1, 2011

January 2011

• DNase - DNase C.gigas RNA from 20110120, 20110121 and 20110124 • kubu4 • January 29, 2011
• RNA Isolation - Various C.gigas Tissue from 20110111 • kubu4 • January 25, 2011
• RNA Isolation - Various C.gigas Tissue from 20110111 • kubu4 • January 22, 2011
• RNA Isolation - Various C.gigas Tissue from 20110111 • kubu4 • January 21, 2011
• Genomic PCR - C.gigas cyclooxygenase (COX) genomic sequence • kubu4 • January 19, 2011
• Bacterial Dilutions - Determination of Colony Forming Units from Gigas Bacterial challenge (from earlier today) • kubu4 • January 12, 2011
• Gigas Bacterial Challenge - 1hr & 3hr Challenges with Vibrio vulnificus • kubu4 • January 12, 2011

2010

</ul>

December 2010

• SOLiD - Retrieved SOLiD Library Samples from CEG from 20101213 • kubu4 • December 24, 2010
• qPCR - COX qPCR Vibrio Exposure Response Check • kubu4 • December 14, 2010
• qPCR - COX qPCR Primer Test and Tissue Distribution • kubu4 • December 11, 2010
• Restriction Digestions/Ligations - MS-AFLP • kubu4 • December 1, 2010

November 2010

• Restriction Digestions - HpaII and MspI on Mac's C.gigas Samples: Round 1 • kubu4 • November 30, 2010
• EtOH Precipitations - HpaII and MspI 2nd Round Digests from 20101124 • kubu4 • November 30, 2010
• Restriction Digestions - HpaII and MspI on Mac's C.gigas Samples: Round 2 • kubu4 • November 25, 2010
• Phenol:Chloroform Extractions and EtOH Precipitations - HapII and MspI digests from yesterday • kubu4 • November 24, 2010
• Restriction Digestions - HpaII and MspI on Mac's C.gigas gDNA Samples: Round 1 • kubu4 • November 23, 2010

October 2010

• QPX Washes • kubu4 • October 27, 2010
• gDNA Isolation • kubu4 • October 27, 2010
• EtOH Precipitation - Whale gDNA from 20101022 • kubu4 • October 26, 2010
• gDNA Isolation • kubu4 • October 23, 2010
• Received Hard Clam Samples and Live Clams from MBL • kubu4 • October 20, 2010
• Received Hard Clam Samples from Rutgers • kubu4 • October 16, 2010
• qPCR - Test Plate for Opticon 2 • kubu4 • October 13, 2010

September 2010

• Opticon Calibration • kubu4 • September 18, 2010
• qPCR - Hard Clam Primers on cDNA from yesterday • kubu4 • September 10, 2010
• Reverse Transcription - DNased Hard Clam RNA from earlier today • kubu4 • September 9, 2010
• DNase - DNasing Hard Clam RNA from yesterday • kubu4 • September 9, 2010
• EtOH Precipitation - Hard Clam RNA from earlier today • kubu4 • September 8, 2010
• RNA Isolation - Hard Clam Tissues Rec'd from Rutgers on 20100820 • kubu4 • September 8, 2010
• Package - Hard Clam Samples from MBL • kubu4 • September 3, 2010

August 2010

• Package - Hard Clam Samples from Rutgers • kubu4 • August 21, 2010

July 2010

• qPCR - HpaII/MspI Digests from earlier today • kubu4 • July 10, 2010
• Restriction Digests - Various gigas gDNA from earlier today • kubu4 • July 10, 2010
• gDNA Isolation - Various gigas samples (continued from yesterday) • kubu4 • July 10, 2010
• gDNA Isolation - Various gigas samples • kubu4 • July 9, 2010
• MeDIP - SB/WB Fragmented gDNA EtOH precipitation (continued from 20100702) • kubu4 • July 9, 2010
• MeDIP - SB/WB Fragmented gDNA (continued from yesterday) • kubu4 • July 3, 2010
• Restriction Digests - Various gigas gDNAs of Mac's • kubu4 • July 3, 2010
• MeDIP - SB/WB Fragmented gDNA (continued from yesterday) • kubu4 • July 2, 2010
• MeDIP - SB/WB Fragmented gDNA (from 20100625) • kubu4 • July 1, 2010
• Bioanalyzer - Fragmented SB/WB gDNA (from 20100625) • kubu4 • July 1, 2010

June 2010

• gDNA Sonication - SB/WB gDNA pools (prep for MeDIP) from 20100618 • kubu4 • June 26, 2010
• Samples Received - Hard Clam samples from Rutgers and MBL • kubu4 • June 25, 2010
• gDNA Sonication - SB/WB gDNA pools (prep for MeDIP) from earlier today • kubu4 • June 19, 2010
• gDNA Precipitation - SB/WB gDNA pools (prep for MeDIP) • kubu4 • June 19, 2010
• gDNA Isolation - Mac gigas larvae samples: control larvae 6.7.10 and 5-aza tr larvae 6.7.10 • kubu4 • June 9, 2010
• gDNA Isolation - Mac gigas gill samples (continued from yesterday) • kubu4 • June 6, 2010
• gDNA Isolation - Mac gigas gill samples • kubu4 • June 4, 2010

May 2010

• gDNA Isolation - Mac gigas gill samples (continued from yesterday) • kubu4 • May 28, 2010
• Package Rec'd - From NOAA in Connecticut • kubu4 • May 27, 2010
• gDNA Isolation - Mac gigas gill samples • kubu4 • May 27, 2010
• SOLiD ePCR/Templated Bead Prep - Lake Trout Lean library • kubu4 • May 26, 2010
• SOLiD Templated Bead Prep - Yellow perch CT, WB and lake trout Lean libraries (continued from yesterday) • kubu4 • May 13, 2010
• SOLiD ePCRs - Yellow perch CT, WB and lake trout Lean libraries • kubu4 • May 12, 2010
• Package - Hard Clam gill tissue/hemolymph in RNA later • kubu4 • May 5, 2010
• DNA Isolation - Qiagen Kit Comparison • kubu4 • May 5, 2010
• qPCR - V.tubiashii primers test (Vpt A and Vt IGS) • kubu4 • May 3, 2010

April 2010

• Templated Bead Prep SOLiD Libraries - Yellow perch WB, lake trout Lean and Sisco, and herring G/O HWS09 libraries • kubu4 • April 16, 2010
• ePCR SOLiD Libraries - Lake Trout Sisco and Herring G/O HPWS09 libraries (from 20100408) • kubu4 • April 15, 2010
• Templated Bead Prep SOLiD Libraries - Abalone CC, CE pools and yellow perch CT, PQ libraries • kubu4 • April 14, 2010
• ePCR SOLiD Libraries - Yellow perch PQ, WB and Lake Trout Lean libraries (from 20100408) • kubu4 • April 13, 2010
• ePCR SOLiD Libraries - Abalone CC, CE pools and yellow perch CT SOLiD libraries (from 20100408) • kubu4 • April 12, 2010
• cDNA clean up & Bioanalyzer for SOLiD Libraries - Abalone, Yellow Perch, Lake Trout, Herring • kubu4 • April 8, 2010
• Gel Purification & PCR cDNA SOLiD Libraries - Abalone, Yellow Perch, Lake Trout, Herring • kubu4 • April 7, 2010
• Reverse Transcription SOLiD Libraries - Abalone, Yellow Perch, Lake Trout, Herring • kubu4 • April 6, 2010
• Hibridizaton/Ligation SOLiD Libraries - Abalone, Yellow Perch, Lake Trout, Herring • kubu4 • April 5, 2010
• Bioanalyzer Total, mRNA and post-fragmentation SOLiD Libraries - Abalone pools • kubu4 • April 2, 2010
• RNA Precipitation and Fragmentation for SOLiD Libraries - Pooled abalone mRNA (from yesterday) • kubu4 • April 1, 2010

March 2010

• RNA Precipitation & mRNA Isolation for SOLiD Libraries - Pooled abalone total RNA: Carmel control, Carmel exposed • kubu4 • March 31, 2010
• Bioanalyzer for SOLiD Libraries - Fragmented mRNA from Perch, Lake Trout & Herring RNA samples • kubu4 • March 29, 2010
• SOLiD Library Prep - mRNA (perch, lake trout, herring from 20100318) Fragmentation • kubu4 • March 25, 2010
• Bioanalyzer for SOLiD libraries - Total and mRNA from Perch, Lake Trout & Herring RNA samples (CONTINUED from yesterday) • kubu4 • March 18, 2010
• mRNA Precipitation for SOLiD - Perch, Lake Trout, & Herring mRNA (CONTINUED from yesterday) • kubu4 • March 17, 2010
• mRNA Isolation for SOLiD - Perch, Lake Trout, and Herring total RNA • kubu4 • March 16, 2010
• PCR - Test Lexie's Mercenaria 18s contamination issue • kubu4 • March 10, 2010

January 2010

• qPCR - Mac's BB/DH cDNA from 20091223 • kubu4 • January 15, 2010
• SOLiD Bead Titration - Herring fragmented cDNA libraries: 2LHKOD09, 4LHTOG09, 6LHPWS09 • kubu4 • January 14, 2010
• SOLiD ePCRs - Herring cDNA libraries • kubu4 • January 13, 2010
• SOLiD ePCR - Herring fragmented cDNA library: 2LHKOD09 • kubu4 • January 11, 2010
• qPCRs - Mac's BB/DH cDNA from 20091223 • kubu4 • January 11, 2010
• SOLiD Bead Titration - Herring fragmented cDNA library 3LHSITK09 (CONTINUED from ePCR yesterday) • kubu4 • January 8, 2010
• SOLiD ePCR - Herring fragmented cDNA library: 3LHSITK09 • kubu4 • January 7, 2010
• SOLiD Bead Titration - Herring fragmented cDNA library 3LHSITK09(CONTINUED from ePCR yesterday) • kubu4 • January 7, 2010
• qPCRs - Tim's Adult Gigas gill cDNA (from 20091009) • kubu4 • January 6, 2010
• SOLiD ePCR - Herring fragmented cDNA library: 3LHSITK09 (from 20091209) • kubu4 • January 6, 2010
• qPCRs - Tim's Adult Gigas gill cDNA (from 20091009) • kubu4 • January 5, 2010

2009

</ul>

December 2009

• qPCR - BB & DH cDNA (from 20091223) • kubu4 • December 31, 2009
• qPCRs - BB & DH cDNA (from 20091223) • kubu4 • December 30, 2009
• qPCR - BB & DH cDNA (from 20091223) • kubu4 • December 29, 2009
• Alaska sockeye salmon sampling (with Seebs): Family #13 • kubu4 • December 29, 2009
• qPCR - BB & DH cDNA (from 20091223) and Emma primer sets for testing • kubu4 • December 29, 2009
• qPCRs - BB & DH cDNA (from 20091223) • kubu4 • December 28, 2009
• qPCRs - BB & DH cDNA (from yesterday) • kubu4 • December 24, 2009
• Sequencing - Mac methylation samples, Sam rhodopsin samples, Lisa samples • kubu4 • December 24, 2009
• qPCR - BB & DH cDNA (from earlier today) • kubu4 • December 23, 2009
• Reverse Transcription - BB & DH DNased RNA (from 20090514) • kubu4 • December 23, 2009
• PCR - Sepia cDNA • kubu4 • December 18, 2009
• PCR - Sepia cDNA • kubu4 • December 17, 2009
• PCR - Sepia cDNA and DNased RNA • kubu4 • December 17, 2009
• PCR - Sepia cDNA (from yesterday) • kubu4 • December 16, 2009
• Reverse Transcription - Abalone 07:12 DNased RNA (from 20090623) • kubu4 • December 16, 2009
• Reverse Transcription - Sepia DNased RNA • kubu4 • December 15, 2009
• Bioanalyzer - Herring Liver cDNA for SOLiD Libraries • kubu4 • December 12, 2009
• Emulsion PCR - Herring Liver cDNA for SOLiD Libraries • kubu4 • December 10, 2009
• Reverse Transcription - Herring Liver mRNA for SOLiD Libraries • kubu4 • December 10, 2009
• RNA Adapter Hybridization and Ligation - Herring Liver mRNA for SOLiD Libraries • kubu4 • December 9, 2009
• RNA Fragmentation - Herring Liver mRNA for SOLiD Libraries • kubu4 • December 8, 2009
• RNA Isolation - Sepia samples • kubu4 • December 5, 2009
• Sequencing - Dungan Isolates, Lake Trout HRM and Emma DD cloning • kubu4 • December 4, 2009
• mRNA Precipitation - Herring Liver mRNA for SOLiD Libraries (continued from yesterday) • kubu4 • December 4, 2009
• Hard Clam Challenge - QPX Strain S-1 (continued from yesterday) • kubu4 • December 3, 2009
• RNA Precipitation - Herring Liver RNA for SOLiD Libraries (continued from yesterday) • kubu4 • December 3, 2009
• RNA Precipitation - Herring Liver RNA for SOLiD Libraries • kubu4 • December 2, 2009
• Hard Clam Challenge - QPX Strain S-1 • kubu4 • December 2, 2009
• MBL Shipment - Hard Clam gill tissue in RNA Later • kubu4 • December 2, 2009

November 2009

• MBL Shipment - Sepia tissue samples • kubu4 • November 26, 2009
• MBL Shipment - Hard Clams • kubu4 • November 25, 2009
• Herring 454 Data • kubu4 • November 20, 2009
• MBL Shipment - MV oysters/cod • kubu4 • November 20, 2009
• PCR - "Unknown" Dungans/Lyons • kubu4 • November 19, 2009
• PCR - "Unkown" Dungans/Lyons • kubu4 • November 18, 2009
• Hard Clams - Shipment from Rutgers • kubu4 • November 14, 2009
• Sequencing - Lake Trout HRM • kubu4 • November 11, 2009
• Oyster CO2/Mechanical Stress - Water quality • kubu4 • November 6, 2009

October 2009

• Sample Submissions to MoGene for 454 Analysis - Herring Liver and Testes mRNA • kubu4 • October 28, 2009
• mRNA Isolation - Herring gonad/ovary RNA (from 20091023) • kubu4 • October 28, 2009
• RNA Precipitation - Herring gonad/ovary RNA (from 20091023) • kubu4 • October 27, 2009
• mRNA Isolation - Herring Liver RNA (from 20091021) • kubu4 • October 27, 2009
• RNA Precipitation - Herring Liver Samples • kubu4 • October 24, 2009
• RNA Isolation - Herring Gonad/Ovary Samples • kubu4 • October 24, 2009
• RNA Isolation - Herring Gonad/Ovary Samples • kubu4 • October 23, 2009
• RNA Isolation - Herring Liver Samples • kubu4 • October 22, 2009
• RNA Isolation - Herring Liver Samples (LHPWS09 1-6) • kubu4 • October 21, 2009
• qPCRs - Tim's adult gigas challenge cDNA (from 20091009) • kubu4 • October 14, 2009
• qPCR - Tim's adult gigas challenge cDNA (from 20091009) • kubu4 • October 13, 2009
• qPCR - Tim's adult gigas challenge cDNA (from today) • kubu4 • October 10, 2009
• Reverse Transcription - Tim's adult gigas challenge DNased RNA (from 20091008) • kubu4 • October 10, 2009
• qPCR - Tim's adults gigas challenge re-DNased RNA (from today) • kubu4 • October 10, 2009
• DNase Treatment - Re-DNase of Tim's adult gigas challenge RNA (from yesterday) • kubu4 • October 10, 2009
• qPCR - Tim's adults gigas challenge DNased RNA (from today) • kubu4 • October 9, 2009
• qPCR - Tim's adults gigas challenge DNased RNA (from today) • kubu4 • October 9, 2009
• DNase Treatment - Tim's adult gigas challenge RNA (from 20090930) • kubu4 • October 9, 2009
• Bioanalyzer Submission - Trout RBC, Colleen's gigas GE sample, Mac's DH/BB PCR for SOLiD WTK • kubu4 • October 8, 2009
• Reverse Transcription/cDNA purification/Emulsion PCR - Ligation rxns of trout fragmented RNA for SOLiD WTK (from yesterday) • kubu4 • October 7, 2009
• Adapter Ligation - Rick's trout fragmented control/poly I:C samples for SOLiD WTK • kubu4 • October 6, 2009
• qPCR - Tim's adults gigas challenge DNased RNA (from 20091002) • kubu4 • October 6, 2009
• DNase Treatment - Tim's adult gigas challenge RNA (from 20090930) • kubu4 • October 3, 2009
• qPCRs - Check gDNA contamination with EF1 & 18s primers in gigas gill RNA (from yesterday) • kubu4 • October 2, 2009
• RNA Isolation - Tim's adult gigas challenge samples • kubu4 • October 1, 2009

September 2009

• Bioanalyzer Submission - Rick's trout RBC samples (various dates) • kubu4 • September 30, 2009
• RNA Fragmentation - Rick's trout RBC samples prepped earlier today • kubu4 • September 30, 2009
• EtOH Precipitation - Rick's trout Ribosomoal-depleted RNA for SOLiD WTK (from today) • kubu4 • September 29, 2009
• Ribosomal-depleted RNA - Rick's trout RBC samples for the SOLiD WTK • kubu4 • September 29, 2009
• RNA Fragmentation - Rick's trout RBC samples prepped earlier today (see below) • kubu4 • September 24, 2009
• mRNA Isolation - Rick's trout RBC samples previously treated with Ribominus Kit (by Mac) • kubu4 • September 24, 2009
• mRNA Isolation - Gigas BB and DH samples previously treated with Ribominus Kit (by Mac) • kubu4 • September 19, 2009
• mRNA Isolation - Gigas BB and DH samples previously treated with Ribominus Kit (by Mac) • kubu4 • September 17, 2009
• HRMs - Lake Trout SNPs (HRM_white-05 & HRM_white_06) • kubu4 • September 16, 2009
• HRMs - Lake Trout SNPs (HRM_white-03 & HRM_white-04) • kubu4 • September 11, 2009
• HRM - Lake Trout SNPs (HRM_white-02) • kubu4 • September 10, 2009
• HRM - Lake Trout SNPs (HRM-white-01) • kubu4 • September 4, 2009
• qPCR - HRM Lake Trout SNP primer test • kubu4 • September 2, 2009

August 2009

• Primers - Lake Trout Primers for HRM • kubu4 • August 27, 2009
• qPCR - Gigas gDNA test of recalibrated Opticon 2 • kubu4 • August 27, 2009
• qPCR - Recalibration of Opticon 2 • kubu4 • August 26, 2009
• DNA Precipitation - C.pugetti DNA for JGI submission (continued from yesterday) • kubu4 • August 26, 2009
• DNA Precipitation - C.pugetti DNA for JGI submission • kubu4 • August 25, 2009
• qPCR - Additional Calibration test of Opticon 2 • kubu4 • August 24, 2009
• qPCR - Carita Primer Test for High Resolution Melt (HRM) Curve Analysis • kubu4 • August 17, 2009
• qPCR - Calibration test of Opticon 2 • kubu4 • August 13, 2009
• qPCR - Calibration test of Opticon 2 • kubu4 • August 6, 2009

July 2009

• Bacteria - C.pugetti culture (from 20090713) • kubu4 • July 23, 2009
• qPCR - Gigas DNA for Opticon testing • kubu4 • July 22, 2009
• RT Rxns - H.crach DNased RNA (from 20090623) • kubu4 • July 22, 2009
• NanoDrop - H.crach DNased RNA (from 20090623) • kubu4 • July 21, 2009
• qPCR - Abalone cDNA (07:12 set from 3/3/2009 by Lisa) and DNased RNA (from 20090623) • kubu4 • July 20, 2009
• qPCR - Abalone gDNA (H.crach 06:7-1) • kubu4 • July 17, 2009
• qPCR - Abalone cDNA (07:12 set from 3/3/2009 by Lisa) and DNased RNA (from 20090623) • kubu4 • July 17, 2009
• qPCR - Abalone cDNA (07:12 set from 3/3/2009 by Lisa) and DNased RNA (from 20090623) • kubu4 • July 17, 2009
• qPCR - Abalone gDNA • kubu4 • July 16, 2009
• qPCR - Abalone RNA/DNased RNA & "dirty" and "clean" cDNA • kubu4 • July 15, 2009
• PCR - Dungan isolate (MIE-14v) gDNA from 20090708 • kubu4 • July 13, 2009
• Bacteria - C.pugetti large culture • kubu4 • July 13, 2009
• qPCR - Abalone gDNA/cDNA • kubu4 • July 11, 2009
• qPCR - DNased Abalone Dg RNA from 20090625 • kubu4 • July 10, 2009
• DNA Precipitation CONTINUED - Dungan MIE-14v gDNA from yesterday • kubu4 • July 9, 2009
• PCR - Bay/Sea Scallop DNA • kubu4 • July 9, 2009
• qPCR - DNased Abalone Dg RNA from 20090625 • kubu4 • July 8, 2009
• DNA Precipitation - Dungan MIE-14v gDNA from earlier today • kubu4 • July 7, 2009
• gDNA Isolation - Dungan isolate MIE-14v • kubu4 • July 7, 2009
• qPCR - MV hemocyte cDNA from 20090614 • kubu4 • July 7, 2009
• Spec Reading - C.pugetti gDNA from 20090526 • kubu4 • July 6, 2009
• qPCR - MV hemocyte cDNA from 20090614 • kubu4 • July 6, 2009
• Bacteria - C. pugetti liquid cultures • kubu4 • July 6, 2009
• qPCR - MV hemocyte cDNA from 20090614 • kubu4 • July 2, 2009
• qPCR - MV hemocyte cDNA from 20090614 • kubu4 • July 1, 2009
• qPCR - MV hemocyte cDNA from 20090614 • kubu4 • July 1, 2009
• qPCR - MV hemocyte cDNA from 20090614 • kubu4 • July 1, 2009

June 2009

• qPCRs - MV hemocyte cDNA from 20090614 • kubu4 • June 30, 2009
• qPCRs - MV hemocyte cDNA from 20090614 • kubu4 • June 29, 2009
• qPCR - MV hemocyte cDNA from 20090614 • kubu4 • June 26, 2009
• qPCR - Abalone Dg DNased RNA from yesterday and earlier today • kubu4 • June 25, 2009
• DNase Treatment - Abalone Dg RNA • kubu4 • June 25, 2009
• qPCRs - MV hemocyte cDNA from 20090614 • kubu4 • June 24, 2009
• DNase Treatment - Abalone Dg RNA (07:12 set) • kubu4 • June 24, 2009
• EtOH Precipitation - DNased Abalone Dg RNA from yesterday AND the 07:12 set (DNased by Lisa 20090306) • kubu4 • June 23, 2009
• qPCR - MV hemocyte cDNA from 20090614 • kubu4 • June 23, 2009
• qPCR - DNased Abalone Dg RNA from earlier today AND the 07:12 set (DNased by Lisa 20090306) • kubu4 • June 23, 2009
• DNase Treatment - Abalone Dg DNased RNA 20090610 • kubu4 • June 23, 2009
• qPCR - MV hemocyte cDNA from 20090614 • kubu4 • June 19, 2009
• qPCR - MV hemocyte cDNA from 20090614 • kubu4 • June 18, 2009
• qPCR - MV hemocyte cDNA: Test Immomix (SYTO13) vs. Strategene SYBR • kubu4 • June 16, 2009
• qPCR - MV hemocyte cDNA from yesterday • kubu4 • June 16, 2009
• Reverse Transcription - MV hemocyte DNased RNA from 20090612 • kubu4 • June 15, 2009
• qPCR - DNased MV hemocyte RNA from earlier today AND Turbo kit test • kubu4 • June 13, 2009
• DNase Treatment - MV hemocyte RNA from yesterday • kubu4 • June 13, 2009
• DNase Treatment - MV hemocyte RNA from earlier today • kubu4 • June 12, 2009
• RNA Isolation - Martha's Vineyard (MV) hemocytes • kubu4 • June 12, 2009
• qPCR - Re-DNased abalone Dg RNA from earlier today • kubu4 • June 11, 2009
• qPCR - Re-DNased abalone Dg RNA from earlier today • kubu4 • June 11, 2009
• DNase Treatment - Abalone Dg DNased RNA from 20090605 • kubu4 • June 11, 2009
• PCR - C.pugetti gDNA from 20090526 • kubu4 • June 10, 2009
• PCR - C.pugetti gDNA from 20090513 & 20090526 • kubu4 • June 9, 2009
• qPCR - Re-DNased abalone Dg RNA from earlier today • kubu4 • June 9, 2009
• DNase Treatment - Abalone Dg DNased RNA from 20090605 • kubu4 • June 9, 2009
• Bacteria - C.pugetti culture (1x 1L) • kubu4 • June 6, 2009
• qPCR - DNased abalone Dg RNA from earlier today • kubu4 • June 6, 2009
• DNase Treatment - Abalone Dg RNA isolated yesterday and from 20090518 • kubu4 • June 6, 2009
• RNA Isolation - Abalone Dg Project Samples • kubu4 • June 5, 2009
• DNase Treatment - Abalone Dg RNA isolated yesterday • kubu4 • June 4, 2009
• PCR - C.pugetti DNA from 20090513 & 20090526 • kubu4 • June 3, 2009
• RNA Isolation - Abalone Dg Project • kubu4 • June 3, 2009
• PCR - C.pugetti DNA from 20090513 & 20090526 • kubu4 • June 2, 2009
• DNA Gel - JGI QC check of C. pugetti DNA from 20090526 • kubu4 • June 2, 2009

May 2009

• gDNA Isolation - C. pugetti (from 20090518) • kubu4 • May 27, 2009
• DNA Methylation Test - Gigas site gDNA (BB & DH) from 20090515 • kubu4 • May 20, 2009
• RNA Isolation - Abalone Dg Project samples • kubu4 • May 18, 2009
• C.pugetti - Liquid Cultures • kubu4 • May 18, 2009
• gDNA Isolation - Gigas Dermo Samples • kubu4 • May 15, 2009
• gDNA Isolation - Mac's BB and DH site samples • kubu4 • May 15, 2009
• Reverse Transcription - Mac's gigas DNased RNA from 20090512 • kubu4 • May 14, 2009
• gDNA Isolation - C.pugetti • kubu4 • May 13, 2009
• qPCR - Mac's gigas DNased RNA from earlier today • kubu4 • May 12, 2009
• DNase Treatment (Rigorous!) - Mac's gigas RNA/Re-DNased RNA from 20090507 & 20090508, respectively • kubu4 • May 12, 2009
• DNA Isolation - Mac's gigas samples from 20090505 & 20090506 • kubu4 • May 11, 2009
• qPCR - Re-DNased oyster RNA from today • kubu4 • May 8, 2009
• DNase Treatment - Oyster RNA from yesterday • kubu4 • May 8, 2009
• qPCR - DNased oyster RNA from earlier today • kubu4 • May 7, 2009
• DNase Treatment - Oyster RNA from today • kubu4 • May 7, 2009
• RNA Isolation - Mac's oyster tissues (BB and DH) (CONTINUED from yesterday) • kubu4 • May 7, 2009
• RNA Isolation - Mac's oyster tissues (BB and DH) (CONTINUED from yesterday) • kubu4 • May 6, 2009
• Bacteria - C. pugetti liquid cultures • kubu4 • May 5, 2009
• RNA Isolation - Mac's oyster tissues (BB and DH) • kubu4 • May 5, 2009
• Bacteria - C. pugetti liquid cultures • kubu4 • May 1, 2009

April 2009

• Bacteria - C. pugetti plate (from 20090424) • kubu4 • April 30, 2009
• Bacteria - C. pugetti plate (from 20090424) • kubu4 • April 29, 2009
• Bacteria - C. pugetti liquid culture • kubu4 • April 27, 2009
• Bacteria - C. pugetti plate • kubu4 • April 24, 2009
• Reverse Transcription - cDNA from DNased Abalone RNA from 20090420 • kubu4 • April 22, 2009
• qPCR - Abalone DNased RNA from yesterday • kubu4 • April 21, 2009
• Bacteria - C. pugettii culture CONTINUED (from 20090419) • kubu4 • April 21, 2009
• gDNA Removal - Abalone RNA from 20090402 and 20090331 • kubu4 • April 20, 2009
• Bacteria - C. pugettii culture • kubu4 • April 19, 2009
• Sequencing - Dungan isolates • kubu4 • April 17, 2009
• PCR - Two new Dungan isolates • kubu4 • April 16, 2009
• qPCR - Rab7_SYBR primers on abalone RNA and DNased RNA • kubu4 • April 15, 2009
• PCR - Two new Dungan isolates from earlier today • kubu4 • April 15, 2009
• gDNA Isolation - Two new Dungan isolates • kubu4 • April 15, 2009
• PCR - Test QT Kit with No RT Abalone rxns from 20090408 • kubu4 • April 14, 2009
• PCR - Bay/Sea scallop gDNAs • kubu4 • April 14, 2009
• PCR - Bay/Sea scallop gDNA isolated earlier today • kubu4 • April 13, 2009
• gDNA Isolation - Bay/Sea Scallop and hybrid samples • kubu4 • April 13, 2009
• PCR - Abalone gDNA/RNA/cDNA w/new TOLLIP primer • kubu4 • April 10, 2009
• PCR - Old Dungan isolates #1-35 w/EukA/B primers • kubu4 • April 10, 2009
• PCR - Bay/Sea scallop hybrids • kubu4 • April 10, 2009
• PCR - Dungan isolates from 20090402 with Euk primers • kubu4 • April 9, 2009
• qPCR - Check DNased abalone RNA (by Lisa) for gDNA • kubu4 • April 9, 2009
• qPCR - Repeat (modified) of yesterday's abalone cDNA check • kubu4 • April 9, 2009
• qPCR - Abalone cDNA (QT) from earlier today • kubu4 • April 8, 2009
• cDNA - Abalone RNA from 20090331 & 20090402 • kubu4 • April 8, 2009
• PCR - New Dungan isolates • kubu4 • April 6, 2009
• PCR - New Dungan isolates • kubu4 • April 3, 2009
• qPCR - Abalone RNA, check for gDNA • kubu4 • April 3, 2009
• gDNA Isolation - New Dungan isolates • kubu4 • April 2, 2009
• RNA Isolation - Abalone digestive gland samples • kubu4 • April 2, 2009

March 2009

• RNA Isolation - Abalone digestive gland samples • kubu4 • March 31, 2009
• RNA Isolation - Abalone digestive gland samples • kubu4 • March 27, 2009
• qPCR - Virginica cDNA (see workup sheet below for more info regarding cDNA) • kubu4 • March 24, 2009
• mRNA Sample Submission Hard clam gill #1 mRNA from 20090313 • kubu4 • March 17, 2009
• mRNA Isolation - hard clam gill #1 continued from yesterday • kubu4 • March 14, 2009
• mRNA Isolation - hard clam gill #1 DNased RNA from today • kubu4 • March 13, 2009
• RNA Precipitation - Hard clam gill #1 RNA from 20080819 • kubu4 • March 13, 2009
• qPCR - Repeat of qPCR from earlier today with fresh primer working stocks • kubu4 • March 3, 2009
• qPCR - Repeat of 20090227 qPCR with clean water • kubu4 • March 3, 2009

February 2009

• qPCR - New 16s primers for V.tubiashii Control vs. Autoclaved gigas samples (see 20090224) • kubu4 • February 28, 2009
• qPCR - Replicate of V.tubiashii Control vs. Autoclaved gigas samples (see yesterday) • kubu4 • February 26, 2009
• qPCR - V.tubiashii Control vs. Autoclaved gigas samples (see below) • kubu4 • February 25, 2009
• Reverse Transcription - V.tubiashii DNAsed RNA (from yesterday) • kubu4 • February 25, 2009
• RNA Isolation - V.tubiashii samples from autoclaved gigas exposure (from 20081218) • kubu4 • February 24, 2009
• Epigenetics Experiment - Gigas treatment • kubu4 • February 21, 2009
• Sample Submission - V.tubiashii Mass Spec • kubu4 • February 19, 2009
• Trypsin digestion - Vibrio 2D spots CONTINUED (from yesterday) • kubu4 • February 13, 2009
• Trypsin digestion - Vibrio 2D spots from 20081217 • kubu4 • February 12, 2009
• mRNA - Submission for Agilent Bioanalyzer • kubu4 • February 7, 2009

January 2009

• mRNA - Precipitation continued from yesterday • kubu4 • January 24, 2009
• mRNA Isolation - Hard Clam gill and hemo RNA • kubu4 • January 23, 2009
• RNA - Hard clam hemo RNA (from 20090121) • kubu4 • January 23, 2009
• RNA Isolation - Hard clam hemo (from 20090121) • kubu4 • January 22, 2009
• Bleeding/Tissue Collection - Hard Clams • kubu4 • January 21, 2009
• RNA - Precipitation of Hard Clam Hemo RNA from 20090116 • kubu4 • January 21, 2009
• RNA Isolation - Hard clam gill, hemos • kubu4 • January 17, 2009
• Bleeding - Hard Clams • kubu4 • January 14, 2009
• RNA - Precipitation continued from yesterday • kubu4 • January 14, 2009
• RNA - Reprecipitation of hard clam RNA from yesterday • kubu4 • January 13, 2009
• Bleeding - Hard Clams • kubu4 • January 12, 2009
• RNA Isolation - Hard Clam hemolymph from 20090108, 20090109 • kubu4 • January 12, 2009
• Bleeding - Hard Clams • kubu4 • January 9, 2009
• Bleeding - Hard Clams • kubu4 • January 8, 2009
• PCR - Dungan Isolates • kubu4 • January 7, 2009
• PCR - Dungan Isolates • kubu4 • January 6, 2009
• SDS/PAGE, Western Blot - Test of HSP70 Ab on heat stressed shellfish for FISH441 • kubu4 • January 2, 2009

2008

</ul>

December 2008

• SDS/PAGE, Western Blot - Test of new Western Breeze Kit & HSP70 Ab for FISH441 • kubu4 • December 31, 2008
• RNA Gel - V. tubiashii mRNA samples (from 20081224) • kubu4 • December 29, 2008
• rRNA Removal - V. tubiashii total RNA from yesterday • kubu4 • December 24, 2008
• RNA Isolation - V. tubiashii from challenge (see 20081216) • kubu4 • December 22, 2008
• Vibrio challenge CONTINUED (from yesterday) • kubu4 • December 19, 2008
• Vibrio challenge CONTINUED (from yesterday) • kubu4 • December 18, 2008
• Vibrio challenge CONTINUED (from yesterday) • kubu4 • December 17, 2008
• Vibrio challenge • kubu4 • December 16, 2008
• SDS/PAGE/Western - anti-HSP70 Ab Re-test • kubu4 • December 16, 2008
• SDS/PAGE/Western - Attempt to fix/identify problem(s) with Westerns • kubu4 • December 12, 2008
• SDS/PAGE/Western - anti-HSP70 Ab test CONTINUED (from yesterday) • kubu4 • December 10, 2008
• SDS/PAGE/Western - anti-HSP70 Ab test • kubu4 • December 9, 2008

November 2008

• SDS/PAGE/Western - Purified (His column) FST samples from 20081112 • kubu4 • November 17, 2008
• Sequencing - Y2H colony PCRs from 20081112 • kubu4 • November 14, 2008
• Mass Spec - Band #1 from 20081106 • kubu4 • November 14, 2008
• Western Blot - Purified (His column) decorin, FST, LAP & telethonin • kubu4 • November 13, 2008