AMSS(1) •
BLAST(7) •
Bioanalyzer(10) •
Briline(1) •
CrabMeeting(9) •
DAVID(2) •
DESeq2(2) •
DIA(1) •
DIAOyster(70) •
DataOrganization(11) •
DecaPod(15) •
EncyclopeDIA(1) •
FASTQC(1) •
GOMWU(2) •
GSS(4) •
Genewiz(1) •
GeoduckStripSpawn(7) •
Hackweek(2) •
Kallisto(3) •
Lyophilizer(4) •
MSStats(2) •
MSstats(1) •
MonthlyGoals(1) •
Mox(5) •
Nanodrop(1) •
OneHealth(1) •
PCSGA(1) •
PhD(10) •
Pubathon(3) •
Qubit(22) •
R(11) •
REVIDO(1) •
REVIGO(1) •
RNAIsolation(62) •
RNeasy(10) •
Reading(1) •
SRM(1) •
Sequencing(15) •
Sequncing(1) •
Skyline(14) •
SpeedVac(2) •
Supernatant(2) •
Transrate(1) •
Trinity(5) •
TrizolLS(5) •
WSG mtg(1) •
Walnut(3) •
Zymo(7) •
analyses(6) •
bairdi(156) •
conferences(3) •
dermasterias(9) •
edgeR(1) •
geoduck(5) •
hemolymph(3) •
histology(1) •
paper(1) •
pisaster(9) •
podcast(6) •
pycnopodia(9) •
pydnopodia(1) •
qPCR(1) •
staging(1) •
thesis(9)
AMSS 1
- January 2020 Goals • January 6, 2020
BLAST 7
- BLAST nt taxonomy with C bairdi had no taxonomy data • December 17, 2018
- BLAST on Hummingbird and Transrate • November 12, 2018
- BLAST really running on Mox, 2015 Oysterseed new plan • November 8, 2018
- BLAST with bad Trinity fasta, R plan for adding Qubit data, and Testing out RNeasy Plus Mirco Kit • October 31, 2018
- BLASTn with Blue Crab and Prep for GSS Poster • November 13, 2018
- First Attempts- Trying new BLAST +2.81 with new taxid options • January 15, 2019
- Sent BLAST to Mox, and Plan for rest of Week • November 6, 2018
Bioanalyzer 10
- Bairdi RNA - Bioanalyzer and Nanodrop, Begin analyses for GSS - Kallisto • November 6, 2019
- Bioanalyzer Results - batch of cold, infected day 26 • December 14, 2018
- Bioanalyzer and Pubathon • May 8, 2018
- Crab Meeting and Bioanalyzer • May 3, 2018
- DNA-free, Qubit, and Bioanalyzer Plan; Kallisto work • November 7, 2019
- Make Taxonomy Pie Charts in R • November 30, 2018
- My Bioanalyzer and Sam's RNA Clean-up Kit and RNeasy Plus Mini Kit results • July 31, 2018
- Plan for R and Bioanalyzer results • October 8, 2018
- RNeasy Test Bioanalyzer Results • November 16, 2018
- Still no clear RNA bands on Bioanalyzer; Also working to get diff. exp. for GSS • November 8, 2019
Briline 1
- Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line • November 26, 2018
CrabMeeting 9
- 2015 Oysterseed Plan and Crab Meeting Notes • December 6, 2018
- Crab Meeting • September 6, 2018
- Crab Meeting • March 1, 2018
- Crab Meeting Notes • July 29, 2019
- Crab Meeting and Bioanalyzer • May 3, 2018
- DNA-free, Qubit, and Bioanalyzer Plan; Kallisto work • November 7, 2019
- DecaPod Season 1 Ep 11 - Crab Mtg • September 7, 2018
- Notes from Crab Meeting • July 5, 2018
- Trinity failed; Re-run, and Notes from Crab Meeting • November 1, 2018
DAVID 2
- Oysterseed DIA - New Analyses and wrapping up paper • September 27, 2019
- Oysterseed DIA - trying to characterize list of detected proteins in relation to _C. gigas_ proteome • September 30, 2019
DESeq2 2
- Crab Analyses Progress • June 17, 2020
- GSS 2019 Preparations - Differential Expression between infected and uninfected • November 12, 2019
DIA 1
- Oyster Paper Updates • April 27, 2021
DIAOyster 70
- 2015 C. gigas oysterseed DIA update • December 10, 2018
- 2015 DIA Oysterseed Paper Progress • March 25, 2019
- 2015 Oysterseed DIA Analysis Update • January 12, 2018
- 2015 Oysterseed DIA MSStats Figures Progress • January 7, 2019
- 2015 Oysterseed DIA meeting notes • February 8, 2018
- 2015 Oysterseed Plan and Crab Meeting Notes • December 6, 2018
- 2015 Oysterseed Skyline questions • June 12, 2018
- 2nd Half of March goals • March 13, 2019
- Annotated Protein List from MS Stats with set thresholds... in progress • April 5, 2019
- April 2020 Goals • May 1, 2020
- April 2020 Goals • January 4, 2020
- April Goals • April 1, 2019
- August Goals • August 1, 2018
- BLAST really running on Mox, 2015 Oysterseed new plan • November 8, 2018
- Bairdi RNA extractions- other methods to try; Plan for Week • April 8, 2019
- Crab Pools and Skyline Update • July 18, 2018
- Crab RNA Isolation and DIA Oyster Updates • March 29, 2018
- DIA 2015 Oysterseed Plan (finish by Apr 17) • March 20, 2019
- DIA Oysterseed Project - Finishing up Paper and cleaning up repo - in progress • August 23, 2019
- DIA analysis 2015 Cg seed continued • December 14, 2018
- DIA protocol, and Next Steps • December 7, 2018
- December 2019 Goals • December 3, 2019
- December Goals • December 1, 2020
- February Goals • February 1, 2021
- February Goals • February 1, 2020
- February Goals • February 1, 2019
- Input from Emma on DIA and RNA isolation starts! • March 13, 2018
- Isolating RNA and trying to check Skyline error rates • March 21, 2018
- January 2019 Goals • January 1, 2019
- January 2020 Goals • January 6, 2020
- January Goals • January 4, 2021
- June 2020 Goals • June 15, 2020
- June Goals • June 1, 2019
- June Goals • June 3, 2018
- Learning more about Trinity and working with large data sets; Update on Skyline issue • June 26, 2018
- March 2020 Goals • March 3, 2020
- May Goals • May 1, 2019
- May Goals • May 3, 2018
- More tables for 2015 _C. gigas_ seed • April 9, 2019
- Moving forward with DIA and plan for RNA isolation • February 27, 2018
- New DEG list comparing temperature - annotation, enrichment; annotation of oyster differentially abundant protein list • May 18, 2020
- New Plan - Lyophilizer; DIA Github Issue • August 13, 2018
- November 2019 Goals • November 1, 2019
- November Goals • November 1, 2018
- October 2019 Goals • October 1, 2019
- October Goals • October 5, 2018
- Oysterseed DIA - New Analyses and wrapping up paper • September 27, 2019
- Oysterseed DIA - trying to characterize list of detected proteins in relation to _C. gigas_ proteome • September 30, 2019
- Oysterseed project progress; Data uploaded to PRIDE • September 12, 2019
- RNA isolation prep and 2015 oysterseed DIA update • January 30, 2018
- RNA isolation protocol testing and DIA analysis re-do • February 16, 2018
- RNA isolation, Podcast thoughts, and DIA protocol • February 15, 2018
- Re-do DIA, thinking about error rate determination • March 14, 2018
- Re-do MS Stats; DIA 2015 Oyster Updates • April 3, 2019
- Re-tried Skyline DIA • August 31, 2018
- Re-visiting error rate in Skyline and figuring out the math in pooling samples for sequencing • June 8, 2018
- Reading and Goals for now until Sept. 25th • August 30, 2018
- Running Qubit for the first time, and continuing DIA analysis • February 20, 2018
- September Goals • September 1, 2019
- September Goals • September 1, 2018
- Skyline DIA with new BLIB made using Walnut • July 27, 2018
- Speed Vac Pt. 1 + Testing Advancing Peak Picking in Skyline • July 17, 2018
- Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line • November 26, 2018
- Still have high error rates in Skyline - posted my issue to the Skyline support page • June 20, 2018
- Trying to understand error rate in Skyline and Running Qubit • March 26, 2018
- Update on Crab Pooling and Plan for next week-ish • June 19, 2018
- Updates on Podcast, DIA, RNA isolation, and Crab data organization • March 9, 2018
- Updates on RNA iso; podcast; DIA • March 12, 2018
- Weekly wrap-up and goals for next week • February 23, 2018
- qPCR Machine arrival and training and Crab data and DIA updates • January 23, 2018
DataOrganization 11
- DIA Next Steps and Crab Data Spreadsheet • January 22, 2018
- Data Organization- info from Pam in excel • April 25, 2018
- Hackweek Day 2 - Crab data sheets • July 30, 2019
- Hemolymph sampling and Qubit data spreadsheet; Samples for Sam to run RNeasy Mini Plus Kit • August 1, 2018
- Learning code to change Factors to numbers • August 2, 2018
- Organizing Crab Qubit results and RNA isolation data - in progress • August 2, 2019
- R and figuring out qPCR and DNA Qubit data • May 14, 2018
- RNA Isolation and Data organization using R • May 2, 2018
- RNA isolation and Data org • April 26, 2018
- RNA isolations for warm day 12 and master data file organization • May 23, 2018
- Weekly Goals • May 22, 2018
DecaPod 15
- April Goals • April 5, 2018
- Bioanalyzer and Pubathon • May 8, 2018
- Cold, Infected Pool with RNeasy and DecaPod S1E13 • November 21, 2018
- Crab Project Updates • April 10, 2018
- Crab RNA Isolation and DIA Oyster Updates • March 29, 2018
- DecaPod Season 1 Ep 11 - Crab Mtg • September 7, 2018
- DecaPod Submitted to Apple, RNA Extraction plan for Mon/Tues • September 28, 2018
- Qubit results and DecaPod episodes • April 6, 2018
- RNA Isolation and DecaPod S1E6 • April 29, 2018
- RNA isolation, Qubit, DecaPod updates • April 20, 2018
- Reading up on Trinity and Interviewed Genevieve Johnson for DecaPod • June 21, 2018
- Update on Crab Pooling and Plan for next week-ish • June 19, 2018
- Updates on RNA iso; podcast; DIA • March 12, 2018
- Weekly Goals • May 22, 2018
- Weekly goals • April 15, 2018
EncyclopeDIA 1
- Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line • November 26, 2018
FASTQC 1
- RNA extraction and Running .fastq sequence files through FASTQC • October 19, 2018
GOMWU 2
- Tried some more GO-MWU stuff - not great - switching gears • April 21, 2020
- Trying GO-MWU with 2019 crab data • April 20, 2020
GSS 4
- BLASTn with Blue Crab and Prep for GSS Poster • November 13, 2018
- Bairdi RNA - Bioanalyzer and Nanodrop, Begin analyses for GSS - Kallisto • November 6, 2019
- GSS 2019 Preparations - Differential Expression between infected and uninfected • November 12, 2019
- Submitted GSS poster, and my goals for Th and F • November 14, 2018
Genewiz 1
- Sent samples to Genewiz • February 12, 2020
GeoduckStripSpawn 7
- Day 1 Geoduck Stripspawn Project at Taylor Shellfish Hathcery - Quilcene, WA • May 29, 2019
- Day 1 of Trial 2 of Geoduck Stripspawn experiment - KCl dose + duration • June 10, 2019
- Day 2 Geoduck Stripspawn Project at Taylor - not great results • May 31, 2019
- Geoduck Egg Development - 3 days later • June 10, 2019
- Geoduck Egg Development Test at Taylor Hatchery • June 7, 2019
- June Goals • June 1, 2019
- Sampling for D-hinge development • June 12, 2019
Hackweek 2
- Hackweek Day 1 • June 4, 2018
- Hackweek Day 2 - Crab data sheets • July 30, 2019
Kallisto 3
- Bairdi RNA - Bioanalyzer and Nanodrop, Begin analyses for GSS - Kallisto • November 6, 2019
- DNA-free, Qubit, and Bioanalyzer Plan; Kallisto work • November 7, 2019
- Still no clear RNA bands on Bioanalyzer; Also working to get diff. exp. for GSS • November 8, 2019
Lyophilizer 4
- Crab Meeting • September 6, 2018
- New Plan - Lyophilizer; DIA Github Issue • August 13, 2018
- Samples in Lyophilizer got all over the place • September 11, 2018
- Start Lyophilizing to test new RNA extraction protocol using Tri-reagent • September 10, 2018
MSStats 2
- 2015 Oysterseed DIA MSStats Figures Progress • January 7, 2019
- Re-do MS Stats; DIA 2015 Oyster Updates • April 3, 2019
MSstats 1
- DIA analysis 2015 Cg seed continued • December 14, 2018
MonthlyGoals 1
- September Goals • September 1, 2018
Mox 5
- BLAST really running on Mox, 2015 Oysterseed new plan • November 8, 2018
- Re-run Trinity with correct files • October 30, 2018
- Sent BLAST to Mox, and Plan for rest of Week • November 6, 2018
- Sent First Trinity Assembly Job to Mox! • October 25, 2018
- Worked more on R script for adding Qubit data; Started using Mox • October 23, 2018
Nanodrop 1
- Bairdi RNA - Bioanalyzer and Nanodrop, Begin analyses for GSS - Kallisto • November 6, 2019
OneHealth 1
- November 2019 Goals • November 1, 2019
PCSGA 1
- Crab Project - What I did for PCSGA 2019 • September 25, 2019
PhD 10
- August Goals • August 1, 2023
- I'm Back!! And Starting Grad School!! Again!! • July 18, 2023
- MUSP Day 1 through 5 Update • July 26, 2023
- MUSP Day 12 through 17 Update and Water Transmission (WAT) Prep and Pre-Filtering • August 7, 2023
- MUSP Day 18 through 26 Update and WAT Start and REX Start • August 17, 2023
- MUSP Day 6 and 7 Update • July 28, 2023
- MUSP Day 8 through 11 Update • August 1, 2023
- Notes and Preparation for Multi-Species Experiment • July 20, 2023
- Start Co-housing Multispecies - No disease exposure yet • July 19, 2023
- Start Multi-Species (MUSP) Experiment!! • July 21, 2023
Pubathon 3
- 2021 Pub-a-thon To-Dos and Progress • February 16, 2021
- Bioanalyzer and Pubathon • May 8, 2018
- May Goals • May 3, 2018
Qubit 22
- 6 pooled Crab RNA samples - unsuccessful concentration with Zymo RNA Clean and Concentrator Kit -5 • January 10, 2020
- April Goals • April 5, 2018
- Crab Project Updates • April 10, 2018
- Crab RNA extractions with Qubit results • October 25, 2019
- DNA-free, Qubit, and Bioanalyzer Plan; Kallisto work • November 7, 2019
- More RNA extracted from Day 9 - RNA in all • November 15, 2019
- Qubit results and DecaPod episodes • April 6, 2018
- RNA Isolation Update and Upcoming Goals • April 24, 2018
- RNA Isolation and Data organization using R • May 2, 2018
- RNA Isolation and DecaPod S1E6 • April 29, 2018
- RNA Isolation continued • April 3, 2018
- RNA Isolation info from Sam - Updated RNA isolation protocol; Qubit • March 27, 2018
- RNA Isolation, continued, and plan for tomorrow • April 4, 2018
- RNA Isolations continued • May 1, 2018
- RNA extractions - more day 12 - RNA in 23 / 24 • October 31, 2019
- RNA isolation, Qubit, DecaPod updates • April 20, 2018
- Running Qubit for the first time, and continuing DIA analysis • February 20, 2018
- Second batch of 24 Crab hemolymph samples - RNA extracted and qubit results • October 25, 2019
- Still no clear RNA bands on Bioanalyzer; Also working to get diff. exp. for GSS • November 8, 2019
- Trying out RNA protocol with 6x original protocol's volumes of reagents • July 30, 2018
- Trying to understand error rate in Skyline and Running Qubit • March 26, 2018
- Weekly goals • April 15, 2018
R 11
- BLAST with bad Trinity fasta, R plan for adding Qubit data, and Testing out RNeasy Plus Mirco Kit • October 31, 2018
- Crab Project - try RNeasy Kit on some samples; Adding Qubit data to sample file • October 22, 2018
- Crab RNA-Seq thoughts; Merging columns in R • August 16, 2018
- Learning code to change Factors to numbers • August 2, 2018
- Make Taxonomy Pie Charts in R • November 30, 2018
- Making Pools for RNASeq, and working on an ultimate MASTER crab spreadsheet • July 13, 2018
- New Hemolymp sample and Qubit file; New RNA-seq short-term plan • August 20, 2018
- Plan for R and Bioanalyzer results • October 8, 2018
- R and figuring out qPCR and DNA Qubit data • May 14, 2018
- Streamlining Processing of Adding Qubit data to Master file • August 17, 2018
- Worked more on R script for adding Qubit data; Started using Mox • October 23, 2018
REVIDO 1
- Oysterseed DIA - trying to characterize list of detected proteins in relation to _C. gigas_ proteome • September 30, 2019
REVIGO 1
- Oysterseed DIA - New Analyses and wrapping up paper • September 27, 2019
RNAIsolation 62
- April Goals • April 5, 2018
- August Goals • August 1, 2018
- BLAST with bad Trinity fasta, R plan for adding Qubit data, and Testing out RNeasy Plus Mirco Kit • October 31, 2018
- Bairdi RNA extractions- other methods to try; Plan for Week • April 8, 2019
- Bairdi hemolymph extraction plan (work in progress) • March 14, 2019
- Crab Meeting • March 1, 2018
- Crab Project - try RNeasy Kit on some samples; Adding Qubit data to sample file • October 22, 2018
- Crab Project Updates • April 10, 2018
- Crab RNA Isolation and DIA Oyster Updates • March 29, 2018
- Crab RNA extractions with Qubit results • October 25, 2019
- Day 12 RNA extractions - RNA in all samples! • October 28, 2019
- Day 12, cold and warm, infected, uninfected RNA extractions - RNA in 24/24 samples • November 1, 2019
- DecaPod Submitted to Apple, RNA Extraction plan for Mon/Tues • September 28, 2018
- Error 3 on Centrifuge- Couldn't finish Extraction with TriZol LS Reagent • January 14, 2019
- Extract RNA from 24 samples - Day 9, 12 infected, 12 uninfected; still need to run on Qubit • January 14, 2020
- Extract RNA from non-lyophilized C. bairdi hemolymph • October 5, 2018
- Hemolymph sampling and Qubit data spreadsheet; Samples for Sam to run RNeasy Mini Plus Kit • August 1, 2018
- Input from Emma on DIA and RNA isolation starts! • March 13, 2018
- Isolating RNA and trying to check Skyline error rates • March 21, 2018
- More RNA extracted from Day 9 - RNA in all • November 15, 2019
- More Tri-reagent Extractions • October 10, 2018
- Moving forward with DIA and plan for RNA isolation • February 27, 2018
- My Bioanalyzer and Sam's RNA Clean-up Kit and RNeasy Plus Mini Kit results • July 31, 2018
- Notes on protocol and plan for Crab Project extractions - use info from Sam's notebook posts • October 23, 2019
- Notes, Thoughts, and Ideas on RNA isolation (and thoughts from Sam) • February 3, 2019
- Preliminary Crab Sample Selection for Seq • January 25, 2018
- Preliminary picks for RNA isolation • February 12, 2018
- Qiagen RNeasy Micro Plus Kit with Geoduck hemolymph and oyster tissue • January 26, 2019
- RNA Isolation Update and Upcoming Goals • April 24, 2018
- RNA Isolation and Data organization using R • May 2, 2018
- RNA Isolation and DecaPod S1E6 • April 29, 2018
- RNA Isolation continued • April 3, 2018
- RNA Isolation info from Sam - Updated RNA isolation protocol; Qubit • March 27, 2018
- RNA Isolation, continued, and plan for tomorrow • April 4, 2018
- RNA Isolations continued • May 1, 2018
- RNA extraction and Running .fastq sequence files through FASTQC • October 19, 2018
- RNA extractions - more day 12 - RNA in 23 / 24 • October 31, 2019
- RNA iso with new protocol • March 28, 2018
- RNA isolation • February 28, 2018
- RNA isolation and Data org • April 26, 2018
- RNA isolation prep and 2015 oysterseed DIA update • January 30, 2018
- RNA isolation protocol and plan for tomorrow • February 13, 2018
- RNA isolation protocol testing and DIA analysis re-do • February 16, 2018
- RNA isolation, Podcast thoughts, and DIA protocol • February 15, 2018
- RNA isolation, Qubit, DecaPod updates • April 20, 2018
- RNA isolations for warm day 12 and master data file organization • May 23, 2018
- RNeasy Extraction Day 1 on 24 samples • March 19, 2019
- RNeasy Kit Extraction with 12 samples - RNA in 1/12 • April 3, 2019
- RNeasy Kit Tube 516-2 starting sample testing • February 20, 2019
- RNeasy Kit with hemo pellets using QIAshredder columns • February 15, 2019
- Second batch of 24 Crab hemolymph samples - RNA extracted and qubit results • October 25, 2019
- Supernatant Trizol LS RNA Extraction attempt • February 14, 2019
- Trizol LS Extraction - Qubit results show no detectable RNA • January 17, 2019
- Trizol LS Reagent RNA Extraction Attempt • January 24, 2019
- Trizol LS Reagent RNA extraction using Geoduck hemolymph and oyster tissue • January 26, 2019
- Trying out RNA protocol with 6x original protocol's volumes of reagents • July 30, 2018
- Trying to understand error rate in Skyline and Running Qubit • March 26, 2018
- Updates on Podcast, DIA, RNA isolation, and Crab data organization • March 9, 2018
- Updates on RNA iso; podcast; DIA • March 12, 2018
- Weekly Goals • May 22, 2018
- Weekly goals • April 15, 2018
- Weekly wrap-up and goals for next week • February 23, 2018
RNeasy 10
- BLAST with bad Trinity fasta, R plan for adding Qubit data, and Testing out RNeasy Plus Mirco Kit • October 31, 2018
- Bairdi hemolymph extraction plan (work in progress) • March 14, 2019
- Cold, Infected Pool with RNeasy and DecaPod S1E13 • November 21, 2018
- Hemolymph sampling and Qubit data spreadsheet; Samples for Sam to run RNeasy Mini Plus Kit • August 1, 2018
- Qiagen RNeasy Micro Plus Kit with Geoduck hemolymph and oyster tissue • January 26, 2019
- RNeasy Extraction Day 1 on 24 samples • March 19, 2019
- RNeasy Kit Extraction with 12 samples - RNA in 1/12 • April 3, 2019
- RNeasy Kit Tube 516-2 starting sample testing • February 20, 2019
- RNeasy Kit with hemo pellets using QIAshredder columns • February 15, 2019
- RNeasy Plus Micro Kit Protocol using RNA Carrier and Supernatant • February 13, 2019
Reading 1
- Reading and Goals for now until Sept. 25th • August 30, 2018
SRM 1
- Reading and Goals for now until Sept. 25th • August 30, 2018
Sequencing 15
- 6 pooled Crab RNA samples - unsuccessful concentration with Zymo RNA Clean and Concentrator Kit -5 • January 10, 2020
- Attempt at Concentrating Pooled (made from extra extracted RNA) Samples with the Zymo Microprep kit • December 13, 2019
- Attempt to concentrate test pools using Zymo RNA Clean and Concentrator Kit -5 • January 7, 2020
- Crab Pools and Skyline Update • July 18, 2018
- Crab RNA-Seq thoughts; Merging columns in R • August 16, 2018
- Gave Pooled Sample to the NWGC for Library Prep and RNA-Seq! • August 23, 2018
- Making Pools for RNASeq, and working on an ultimate MASTER crab spreadsheet • July 13, 2018
- New Crab Pooling Plan for RNA Seq • July 2, 2018
- New Hemolymp sample and Qubit file; New RNA-seq short-term plan • August 20, 2018
- Pooled 6 new samples for sequencing • November 22, 2019
- Samples for Sequencing • June 3, 2018
- Sent samples to Genewiz • February 12, 2020
- Submitted 6 pooled crab samples to NWGC for QC • January 31, 2020
- Trying out Walnut; Crab Pool Update • July 26, 2018
- Update on Crab Pooling and Plan for next week-ish • June 19, 2018
Sequncing 1
- Closer to having some pooled libraries! • May 9, 2019
Skyline 14
- 2015 C. gigas oysterseed DIA update • December 10, 2018
- 2015 Oysterseed DIA meeting notes • February 8, 2018
- Crab Pools and Skyline Update • July 18, 2018
- DIA Next Steps and Crab Data Spreadsheet • January 22, 2018
- Determining error rate for DIA 2015 Oysterseed • January 16, 2018
- Finished Determining Error Rate for DIA • January 17, 2018
- New Plan - Lyophilizer; DIA Github Issue • August 13, 2018
- Re-do DIA, thinking about error rate determination • March 14, 2018
- Re-tried Skyline DIA • August 31, 2018
- September Goals • September 1, 2018
- Skyline DIA with new BLIB made using Walnut • July 27, 2018
- Speed Vac Pt. 1 + Testing Advancing Peak Picking in Skyline • July 17, 2018
- Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line • November 26, 2018
- Trying out Walnut; Crab Pool Update • July 26, 2018
SpeedVac 2
- Speed Vac New Pool of 15 Samples • August 22, 2018
- Speed Vac Pt. 1 + Testing Advancing Peak Picking in Skyline • July 17, 2018
Supernatant 2
- RNeasy Plus Micro Kit Protocol using RNA Carrier and Supernatant • February 13, 2019
- Supernatant Trizol LS RNA Extraction attempt • February 14, 2019
Transrate 1
- BLAST on Hummingbird and Transrate • November 12, 2018
Trinity 5
- Learning more about Trinity and working with large data sets; Update on Skyline issue • June 26, 2018
- Re-run Trinity with correct files • October 30, 2018
- Reading up on Trinity and Interviewed Genevieve Johnson for DecaPod • June 21, 2018
- Sent First Trinity Assembly Job to Mox! • October 25, 2018
- Trinity failed; Re-run, and Notes from Crab Meeting • November 1, 2018
TrizolLS 5
- Error 3 on Centrifuge- Couldn't finish Extraction with TriZol LS Reagent • January 14, 2019
- Supernatant Trizol LS RNA Extraction attempt • February 14, 2019
- Trizol LS Extraction - Qubit results show no detectable RNA • January 17, 2019
- Trizol LS Reagent RNA Extraction Attempt • January 24, 2019
- Trizol LS Reagent RNA extraction using Geoduck hemolymph and oyster tissue • January 26, 2019
WSG mtg 1
- DIA 2015 Oysterseed Plan (finish by Apr 17) • March 20, 2019
Walnut 3
- Skyline DIA with new BLIB made using Walnut • July 27, 2018
- Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line • November 26, 2018
- Trying out Walnut; Crab Pool Update • July 26, 2018
Zymo 7
- Crab RNA extractions with Qubit results • October 25, 2019
- Day 12 RNA extractions - RNA in all samples! • October 28, 2019
- Day 12, cold and warm, infected, uninfected RNA extractions - RNA in 24/24 samples • November 1, 2019
- More RNA extracted from Day 9 - RNA in all • November 15, 2019
- Notes on protocol and plan for Crab Project extractions - use info from Sam's notebook posts • October 23, 2019
- RNA extractions - more day 12 - RNA in 23 / 24 • October 31, 2019
- Second batch of 24 Crab hemolymph samples - RNA extracted and qubit results • October 25, 2019
analyses 6
- Annotate 2019 infection status DEG list; short-term paper plan • April 30, 2020
- Crab Analyses Progress • June 17, 2020
- Heatmap Practice • May 19, 2020
- More Crab results - DESeq ABC v GHI; more heatmaps • May 25, 2020
- New DEG list comparing temperature - annotation, enrichment; annotation of oyster differentially abundant protein list • May 18, 2020
- Submitted Thesis Chapters to Committee; Start working with New transcriptome • May 13, 2020
bairdi 156
- 2015 Oysterseed Plan and Crab Meeting Notes • December 6, 2018
- 2nd Half of March goals • March 13, 2019
- 6 pooled Crab RNA samples - unsuccessful concentration with Zymo RNA Clean and Concentrator Kit -5 • January 10, 2020
- Annotate 2019 infection status DEG list; short-term paper plan • April 30, 2020
- April 2020 Goals • May 1, 2020
- April 2020 Goals • January 4, 2020
- April Goals • April 1, 2019
- April Goals • April 5, 2018
- Attempt at Concentrating Pooled (made from extra extracted RNA) Samples with the Zymo Microprep kit • December 13, 2019
- Attempt to concentrate test pools using Zymo RNA Clean and Concentrator Kit -5 • January 7, 2020
- August 2019 Goals • August 1, 2019
- August Goals • August 1, 2018
- BLAST nt taxonomy with C bairdi had no taxonomy data • December 17, 2018
- BLAST on Hummingbird and Transrate • November 12, 2018
- BLAST really running on Mox, 2015 Oysterseed new plan • November 8, 2018
- BLAST with bad Trinity fasta, R plan for adding Qubit data, and Testing out RNeasy Plus Mirco Kit • October 31, 2018
- BLASTn with Blue Crab and Prep for GSS Poster • November 13, 2018
- Bairdi RNA - Bioanalyzer and Nanodrop, Begin analyses for GSS - Kallisto • November 6, 2019
- Bairdi RNA extractions- other methods to try; Plan for Week • April 8, 2019
- Bairdi hemolymph extraction plan (work in progress) • March 14, 2019
- Bioanalyzer Results - batch of cold, infected day 26 • December 14, 2018
- Closer to having some pooled libraries! • May 9, 2019
- Cold, Infected Pool with RNeasy and DecaPod S1E13 • November 21, 2018
- Crab Analyses Progress • June 17, 2020
- Crab Meeting • September 6, 2018
- Crab Meeting Notes • July 29, 2019
- Crab Meeting and Bioanalyzer • May 3, 2018
- Crab Pools and Skyline Update • July 18, 2018
- Crab Project - try RNeasy Kit on some samples; Adding Qubit data to sample file • October 22, 2018
- Crab Project Updates • April 5, 2018
- Crab Project Updates and Next Steps • November 30, 2020
- Crab RNA Isolation and DIA Oyster Updates • March 29, 2018
- Crab RNA extractions with Qubit results • October 25, 2019
- Crab RNA-Seq thoughts; Merging columns in R • August 16, 2018
- Crab Results progress - GOslim transcriptome plot, macropinocytosis list and notes • April 24, 2020
- Create annotated crab transcriptome BLAST `join` with uniprot SP GO • May 6, 2020
- Create list of Trinity_IDs associated with GOslim "Stress response" from annotated crab transcriptome • February 27, 2020
- DNA-free, Qubit, and Bioanalyzer Plan; Kallisto work • November 7, 2019
- Day 12 RNA extractions - RNA in all samples! • October 28, 2019
- Day 12, cold and warm, infected, uninfected RNA extractions - RNA in 24/24 samples • November 1, 2019
- DecaPod Season 1 Ep 11 - Crab Mtg • September 7, 2018
- DecaPod Submitted to Apple, RNA Extraction plan for Mon/Tues • September 28, 2018
- December 2019 Goals • December 3, 2019
- December Goals • December 1, 2020
- Error 3 on Centrifuge- Couldn't finish Extraction with TriZol LS Reagent • January 14, 2019
- Extract RNA from 24 samples - Day 9, 12 infected, 12 uninfected; still need to run on Qubit • January 14, 2020
- Extract RNA from non-lyophilized C. bairdi hemolymph • October 5, 2018
- February Goals • February 1, 2021
- February Goals • February 1, 2020
- February Goals • February 1, 2019
- First Attempts- Trying new BLAST +2.81 with new taxid options • January 15, 2019
- GSS 2019 Preparations - Differential Expression between infected and uninfected • November 12, 2019
- Gave Pooled Sample to the NWGC for Library Prep and RNA-Seq! • August 23, 2018
- Hackweek Day 2 - Crab data sheets • July 30, 2019
- Heatmap Practice • May 19, 2020
- Hemolymph sampling and Qubit data spreadsheet; Samples for Sam to run RNeasy Mini Plus Kit • August 1, 2018
- Input from Emma on DIA and RNA isolation starts! • March 13, 2018
- Isolating RNA and trying to check Skyline error rates • March 21, 2018
- January 2019 Goals • January 1, 2019
- January 2020 Goals • January 6, 2020
- January Goals • January 4, 2021
- June 2020 Goals • June 15, 2020
- June Goals • June 3, 2018
- Learning code to change Factors to numbers • August 2, 2018
- Learning more about Trinity and working with large data sets; Update on Skyline issue • June 26, 2018
- MS Thesis update • November 30, 2020
- Made new crab transcriptome stress response gene list; notes on crab immunity and macropinocytosis • April 29, 2020
- Make Taxonomy Pie Charts in R • November 30, 2018
- Making Pools for RNASeq, and working on an ultimate MASTER crab spreadsheet • July 13, 2018
- March 2020 Goals • March 3, 2020
- May Goals • May 1, 2019
- May Goals • May 3, 2018
- More Crab results - DESeq ABC v GHI; more heatmaps • May 25, 2020
- More RNA extracted from Day 9 - RNA in all • November 15, 2019
- More Tri-reagent Extractions • October 10, 2018
- Moving forward with DIA and plan for RNA isolation • February 27, 2018
- My Bioanalyzer and Sam's RNA Clean-up Kit and RNeasy Plus Mini Kit results • July 31, 2018
- New Crab Pooling Plan for RNA Seq • July 2, 2018
- New DEG list comparing temperature - annotation, enrichment; annotation of oyster differentially abundant protein list • May 18, 2020
- New Hemolymp sample and Qubit file; New RNA-seq short-term plan • August 20, 2018
- New Plan - Lyophilizer; DIA Github Issue • August 13, 2018
- Notes from Crab Meeting • July 5, 2018
- Notes on protocol and plan for Crab Project extractions - use info from Sam's notebook posts • October 23, 2019
- Notes, Thoughts, and Ideas on RNA isolation (and thoughts from Sam) • February 3, 2019
- November 2019 Goals • November 1, 2019
- November Goals • November 1, 2018
- October 2019 Goals • October 1, 2019
- October Goals • October 5, 2018
- Organizing Crab Qubit results and RNA isolation data - in progress • August 2, 2019
- Plan for R and Bioanalyzer results • October 8, 2018
- Podcast and RNA isolation next steps • February 6, 2018
- Podcast thoughts and Crab hemoolymph samples • January 26, 2018
- Pooled 6 new samples for sequencing • November 22, 2019
- Qiagen RNeasy Micro Plus Kit with Geoduck hemolymph and oyster tissue • January 26, 2019
- Qubit results and DecaPod episodes • April 6, 2018
- RNA Isolation Update and Upcoming Goals • April 24, 2018
- RNA Isolation and Data organization using R • May 2, 2018
- RNA Isolation and DecaPod S1E6 • April 29, 2018
- RNA Isolation continued • April 3, 2018
- RNA Isolation info from Sam - Updated RNA isolation protocol; Qubit • March 27, 2018
- RNA Isolation, continued, and plan for tomorrow • April 4, 2018
- RNA Isolations continued • May 1, 2018
- RNA extraction and Running .fastq sequence files through FASTQC • October 19, 2018
- RNA extractions - more day 12 - RNA in 23 / 24 • October 31, 2019
- RNA iso with new protocol • March 28, 2018
- RNA isolation and Data org • April 26, 2018
- RNA isolation protocol testing and DIA analysis re-do • February 16, 2018
- RNA isolation, Podcast thoughts, and DIA protocol • February 15, 2018
- RNA isolation, Qubit, DecaPod updates • April 20, 2018
- RNeasy Extraction Day 1 on 24 samples • March 19, 2019
- RNeasy Kit Extraction with 12 samples - RNA in 1/12 • April 3, 2019
- RNeasy Kit Tube 516-2 starting sample testing • February 20, 2019
- RNeasy Kit with hemo pellets using QIAshredder columns • February 15, 2019
- RNeasy Plus Micro Kit Protocol using RNA Carrier and Supernatant • February 13, 2019
- RNeasy Test Bioanalyzer Results • November 16, 2018
- Re-run Trinity with correct files • October 30, 2018
- Re-visiting error rate in Skyline and figuring out the math in pooling samples for sequencing • June 8, 2018
- Reading and Goals for now until Sept. 25th • August 30, 2018
- Reading up on Trinity and Interviewed Genevieve Johnson for DecaPod • June 21, 2018
- Running Qubit for the first time, and continuing DIA analysis • February 20, 2018
- Samples in Lyophilizer got all over the place • September 11, 2018
- Second batch of 24 Crab hemolymph samples - RNA extracted and qubit results • October 25, 2019
- Sent BLAST to Mox, and Plan for rest of Week • November 6, 2018
- Sent First Trinity Assembly Job to Mox! • October 25, 2018
- Sent samples to Genewiz • February 12, 2020
- September Goals • September 1, 2019
- September Goals • September 1, 2018
- Speed Vac New Pool of 15 Samples • August 22, 2018
- Speed Vac Pt. 1 + Testing Advancing Peak Picking in Skyline • July 17, 2018
- Start Lyophilizing to test new RNA extraction protocol using Tri-reagent • September 10, 2018
- Still no clear RNA bands on Bioanalyzer; Also working to get diff. exp. for GSS • November 8, 2019
- Streamlining Processing of Adding Qubit data to Master file • August 17, 2018
- Submitted 6 pooled crab samples to NWGC for QC • January 31, 2020
- Submitted GSS poster, and my goals for Th and F • November 14, 2018
- Submitted Thesis Chapters to Committee; Start working with New transcriptome • May 13, 2020
- Supernatant Trizol LS RNA Extraction attempt • February 14, 2019
- Thesis Proposal Writing Class • February 21, 2018
- Tried some more GO-MWU stuff - not great - switching gears • April 21, 2020
- Trinity failed; Re-run, and Notes from Crab Meeting • November 1, 2018
- Trizol LS Extraction - Qubit results show no detectable RNA • January 17, 2019
- Trizol LS Reagent RNA Extraction Attempt • January 24, 2019
- Trizol LS Reagent RNA extraction using Geoduck hemolymph and oyster tissue • January 26, 2019
- Trying GO-MWU with 2019 crab data • April 20, 2020
- Trying out RNA protocol with 6x original protocol's volumes of reagents • July 30, 2018
- Trying out Walnut; Crab Pool Update • July 26, 2018
- Trying to understand error rate in Skyline and Running Qubit • March 26, 2018
- Update on Crab Pooling and Plan for next week-ish • June 19, 2018
- Updates on Podcast, DIA, RNA isolation, and Crab data organization • March 9, 2018
- Updates on RNA iso; podcast; DIA • March 12, 2018
- Weekly Goals • May 22, 2018
- Weekly goals • April 15, 2018
- Weekly wrap-up and goals for next week • February 23, 2018
- Worked more on R script for adding Qubit data; Started using Mox • October 23, 2018
- edgeR practice: crab 2019 data • April 15, 2020
- qPCR Machine arrival and training and Crab data and DIA updates • January 23, 2018
conferences 3
- August 2019 Goals • August 1, 2019
- Crab Project - What I did for PCSGA 2019 • September 25, 2019
- January 2020 Goals • January 6, 2020
dermasterias 9
- August Goals • August 1, 2023
- MUSP Day 1 through 5 Update • July 26, 2023
- MUSP Day 12 through 17 Update and Water Transmission (WAT) Prep and Pre-Filtering • August 7, 2023
- MUSP Day 18 through 26 Update and WAT Start and REX Start • August 17, 2023
- MUSP Day 6 and 7 Update • July 28, 2023
- MUSP Day 8 through 11 Update • August 1, 2023
- Notes and Preparation for Multi-Species Experiment • July 20, 2023
- Start Co-housing Multispecies - No disease exposure yet • July 19, 2023
- Start Multi-Species (MUSP) Experiment!! • July 21, 2023
edgeR 1
- edgeR practice: crab 2019 data • April 15, 2020
geoduck 5
- Day 1 of Trial 2 of Geoduck Stripspawn experiment - KCl dose + duration • June 10, 2019
- Day 2 Geoduck Stripspawn Project at Taylor - not great results • May 31, 2019
- Geoduck Egg Development - 3 days later • June 10, 2019
- Geoduck Egg Development Test at Taylor Hatchery • June 7, 2019
- Sampling for D-hinge development • June 12, 2019
hemolymph 3
- Processing Hemolymph • December 20, 2017
- RNA Isolation continued • April 3, 2018
- RNA Isolation, continued, and plan for tomorrow • April 4, 2018
histology 1
- Geoduck Slide Staging for Shelly • December 21, 2020
paper 1
- Oyster Paper Updates • April 27, 2021
pisaster 9
- August Goals • August 1, 2023
- MUSP Day 1 through 5 Update • July 26, 2023
- MUSP Day 12 through 17 Update and Water Transmission (WAT) Prep and Pre-Filtering • August 7, 2023
- MUSP Day 18 through 26 Update and WAT Start and REX Start • August 17, 2023
- MUSP Day 6 and 7 Update • July 28, 2023
- MUSP Day 8 through 11 Update • August 1, 2023
- Notes and Preparation for Multi-Species Experiment • July 20, 2023
- Start Co-housing Multispecies - No disease exposure yet • July 19, 2023
- Start Multi-Species (MUSP) Experiment!! • July 21, 2023
podcast 6
- Crab sample organization and Podcast Audacity Workshop notes • March 2, 2018
- Podcast and RNA isolation next steps • February 6, 2018
- Podcast testing • February 5, 2018
- Podcast thoughts and Crab hemoolymph samples • January 26, 2018
- RNA isolation, Podcast thoughts, and DIA protocol • February 15, 2018
- Updates on Podcast, DIA, RNA isolation, and Crab data organization • March 9, 2018
pycnopodia 9
- August Goals • August 1, 2023
- MUSP Day 1 through 5 Update • July 26, 2023
- MUSP Day 12 through 17 Update and Water Transmission (WAT) Prep and Pre-Filtering • August 7, 2023
- MUSP Day 18 through 26 Update and WAT Start and REX Start • August 17, 2023
- MUSP Day 6 and 7 Update • July 28, 2023
- MUSP Day 8 through 11 Update • August 1, 2023
- Notes and Preparation for Multi-Species Experiment • July 20, 2023
- Start Co-housing Multispecies - No disease exposure yet • July 19, 2023
- Start Multi-Species (MUSP) Experiment!! • July 21, 2023
pydnopodia 1
- I'm Back!! And Starting Grad School!! Again!! • July 18, 2023
qPCR 1
- qPCR Machine arrival and training and Crab data and DIA updates • January 23, 2018
staging 1
- Geoduck Slide Staging for Shelly • December 21, 2020
thesis 9
- April 2020 Goals • May 1, 2020
- February Goals • February 1, 2020
- January 2020 Goals • January 6, 2020
- June 2020 Goals • June 15, 2020
- MS Thesis update • November 30, 2020
- March 2020 Goals • March 3, 2020
- November 2019 Goals • November 1, 2019
- October 2019 Goals • October 1, 2019
- Submitted Thesis Chapters to Committee; Start working with New transcriptome • May 13, 2020