2024
December 2024
- Paper Draft Updates • December 9, 2024
- December Goals • December 2, 2024
November 2024
- November Recap • November 30, 2024
- November Goals • November 1, 2024
October 2024
- Notes from Meeting with Steven; Paper Updates • October 31, 2024
- Multi-Species Data - Transfer and Repository Updates • October 31, 2024
- Pycno Paper Updates - Results and Methods • October 30, 2024
- Meeting Agenda and Action Items - Prep for Halloween Meeting with Steven • October 30, 2024
- Pycno Paper 1 Updates • October 25, 2024
- Writing Retreat Day 2 and 3 • October 23, 2024
- Analyses Continued - Summer 2021 and 2022 - Bonferroni lists; Writing Retreat Day 1 • October 21, 2024
- Data Received - MultiSpecies RNAseq • October 18, 2024
- Analyses - Summer 2022 Results and Comparing to 2021 Results • October 18, 2024
- Analyses - Summer 2021 Results and Short-Term Goals • October 15, 2024
- Analyses - Summer 2021 and 2022 Updates • October 11, 2024
- Updates! • October 10, 2024
- Summer 2021-2022 RNAseq Alignment • October 7, 2024
- Summer 2022 Data Entry, Summer 2021-2022 Work, Multi-Species RNAseq Update • October 2, 2024
- Summer 2022 Data Entry • October 2, 2024
- Summer 2022 Data Entry and 2021/2022 Analyses Update • October 1, 2024
- October Goals • October 1, 2024
September 2024
- Summer 2022 Data Entry • September 30, 2024
- Summer 2021 and Summer 2022 Analyses - Getting Gene Annotations • September 27, 2024
- Summer 2021 and Summer 2022 Analyses - Enrichment • September 20, 2024
- Summer 2021 and Summer 2022 Analyses Status • September 18, 2024
June 2024
- Summer 2021 Experiment B Analyses Update and Progress • June 18, 2024
April 2024
- April 2024 Goals • April 1, 2024
March 2024
- March 2024 Goals • March 1, 2024
February 2024
- Summer 2021 and Summer 2023 Sea Star Wasting Disease Work Updates • February 12, 2024
- January 2024 Recap • February 8, 2024
- February 2024 Goals • February 8, 2024
2023
</ul>December 2023
- December Goals • December 1, 2023
November 2023
- PCA Plots Summer 2022 RNAseq Data • November 29, 2023
- Recap of WSN 2023 and Eelgrass Workshop • November 15, 2023
- November Goals • November 1, 2023
- Start QC and Trimming of Summer 2022 _Pycnopodia helianthoides_ Coelomocyte RNAseq Data • November 1, 2023
- November Goals • November 1, 2023
October 2023
- October Update • October 18, 2023
- October Goals • October 2, 2023
August 2023
- MUSP Day 18 through 26 Update and WAT Start and REX Start • August 17, 2023
- MUSP Day 12 through 17 Update and Water Transmission (WAT) Prep and Pre-Filtering • August 7, 2023
- MUSP Day 8 through 11 Update • August 1, 2023
- August Goals • August 1, 2023
July 2023
- MUSP Day 6 and 7 Update • July 28, 2023
- MUSP Day 1 through 5 Update • July 26, 2023
- Start Multi-Species (MUSP) Experiment!! • July 21, 2023
- Notes and Preparation for Multi-Species Experiment • July 20, 2023
- Start Co-housing Multispecies - No disease exposure yet • July 19, 2023
- I'm Back!! And Starting Grad School!! Again!! • July 18, 2023
2021
</ul>November 2021
- November 2021 Goals • November 1, 2021
July 2021
- July Goals 2021 • July 1, 2021
May 2021
- May Goals • May 3, 2021
April 2021
- Oyster Paper Updates • April 27, 2021
- April Goals • April 1, 2021
March 2021
- Oyster Paper Progress • March 25, 2021
- Oyster Paper Progress - Pubathon To-Dos for next week • March 11, 2021
- March Goals • March 1, 2021
February 2021
- Pubathon - Crab Paper Submitted, Moving on to Oyster Paper • February 26, 2021
- 2021 Pub-a-thon To-Dos and Progress • February 16, 2021
- February Goals • February 1, 2021
January 2021
- How to Create and Publish a Podcast • January 27, 2021
- January Goals • January 4, 2021
2020
</ul>December 2020
- Geoduck Slide Staging for Shelly • December 21, 2020
- December Goals • December 1, 2020
November 2020
- MS Thesis update • November 30, 2020
- Crab Project Updates and Next Steps • November 30, 2020
June 2020
- Crab Analyses Progress • June 17, 2020
- June 2020 Goals • June 15, 2020
May 2020
- More Crab results - DESeq ABC v GHI; more heatmaps • May 25, 2020
- Heatmap Practice • May 19, 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
- Create annotated crab transcriptome BLAST `join` with uniprot SP GO • May 6, 2020
- April 2020 Goals • May 1, 2020
April 2020
- Annotate 2019 infection status DEG list; short-term paper plan • April 30, 2020
- Made new crab transcriptome stress response gene list; notes on crab immunity and macropinocytosis • April 29, 2020
- Crab Results progress - GOslim transcriptome plot, macropinocytosis list and notes • April 24, 2020
- Tried some more GO-MWU stuff - not great - switching gears • April 21, 2020
- Trying GO-MWU with 2019 crab data • April 20, 2020
- edgeR practice: crab 2019 data • April 15, 2020
March 2020
- March 2020 Goals • March 3, 2020
February 2020
- Create list of Trinity_IDs associated with GOslim "Stress response" from annotated crab transcriptome • February 27, 2020
- Sent samples to Genewiz • February 12, 2020
- February Goals • February 1, 2020
January 2020
- Submitted 6 pooled crab samples to NWGC for QC • January 31, 2020
- Extract RNA from 24 samples - Day 9, 12 infected, 12 uninfected; still need to run on Qubit • January 14, 2020
- 6 pooled Crab RNA samples - unsuccessful concentration with Zymo RNA Clean and Concentrator Kit -5 • January 10, 2020
- Attempt to concentrate test pools using Zymo RNA Clean and Concentrator Kit -5 • January 7, 2020
- January 2020 Goals • January 6, 2020
- April 2020 Goals • January 4, 2020
2019
</ul>December 2019
- Attempt at Concentrating Pooled (made from extra extracted RNA) Samples with the Zymo Microprep kit • December 13, 2019
- December 2019 Goals • December 3, 2019
November 2019
- Pooled 6 new samples for sequencing • November 22, 2019
- More RNA extracted from Day 9 - RNA in all • November 15, 2019
- GSS 2019 Preparations - Differential Expression between infected and uninfected • November 12, 2019
- Still no clear RNA bands on Bioanalyzer; Also working to get diff. exp. for GSS • November 8, 2019
- DNA-free, Qubit, and Bioanalyzer Plan; Kallisto work • November 7, 2019
- Bairdi RNA - Bioanalyzer and Nanodrop, Begin analyses for GSS - Kallisto • November 6, 2019
- Day 12, cold and warm, infected, uninfected RNA extractions - RNA in 24/24 samples • November 1, 2019
- November 2019 Goals • November 1, 2019
October 2019
- RNA extractions - more day 12 - RNA in 23 / 24 • October 31, 2019
- Day 12 RNA extractions - RNA in all samples! • October 28, 2019
- Second batch of 24 Crab hemolymph samples - RNA extracted and qubit results • October 25, 2019
- Crab RNA extractions with Qubit results • October 25, 2019
- Notes on protocol and plan for Crab Project extractions - use info from Sam's notebook posts • October 23, 2019
- October 2019 Goals • October 1, 2019
September 2019
- Oysterseed DIA - trying to characterize list of detected proteins in relation to _C. gigas_ proteome • September 30, 2019
- Oysterseed DIA - New Analyses and wrapping up paper • September 27, 2019
- Crab Project - What I did for PCSGA 2019 • September 25, 2019
- Oysterseed project progress; Data uploaded to PRIDE • September 12, 2019
- September Goals • September 1, 2019
August 2019
- DIA Oysterseed Project - Finishing up Paper and cleaning up repo - in progress • August 23, 2019
- Organizing Crab Qubit results and RNA isolation data - in progress • August 2, 2019
- August 2019 Goals • August 1, 2019
July 2019
- Hackweek Day 2 - Crab data sheets • July 30, 2019
- Crab Meeting Notes • July 29, 2019
- July Goals • July 1, 2019
June 2019
- Sampling for D-hinge development • June 12, 2019
- Day 1 of Trial 2 of Geoduck Stripspawn experiment - KCl dose + duration • June 10, 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
May 2019
- Day 2 Geoduck Stripspawn Project at Taylor - not great results • May 31, 2019
- Day 1 Geoduck Stripspawn Project at Taylor Shellfish Hathcery - Quilcene, WA • May 29, 2019
- Closer to having some pooled libraries! • May 9, 2019
- May Goals • May 1, 2019
April 2019
- More tables for 2015 _C. gigas_ seed • April 9, 2019
- Bairdi RNA extractions- other methods to try; Plan for Week • April 8, 2019
- Annotated Protein List from MS Stats with set thresholds... in progress • April 5, 2019
- RNeasy Kit Extraction with 12 samples - RNA in 1/12 • April 3, 2019
- Re-do MS Stats; DIA 2015 Oyster Updates • April 3, 2019
- April Goals • April 1, 2019
March 2019
- 2015 DIA Oysterseed Paper Progress • March 25, 2019
- DIA 2015 Oysterseed Plan (finish by Apr 17) • March 20, 2019
- RNeasy Extraction Day 1 on 24 samples • March 19, 2019
- Bairdi hemolymph extraction plan (work in progress) • March 14, 2019
- 2nd Half of March goals • March 13, 2019
February 2019
- RNeasy Kit Tube 516-2 starting sample testing • February 20, 2019
- RNeasy Kit with hemo pellets using QIAshredder columns • February 15, 2019
- Supernatant Trizol LS RNA Extraction attempt • February 14, 2019
- RNeasy Plus Micro Kit Protocol using RNA Carrier and Supernatant • February 13, 2019
- Notes, Thoughts, and Ideas on RNA isolation (and thoughts from Sam) • February 3, 2019
- February Goals • February 1, 2019
January 2019
- Trizol LS Reagent RNA extraction using Geoduck hemolymph and oyster tissue • January 26, 2019
- Qiagen RNeasy Micro Plus Kit with Geoduck hemolymph and oyster tissue • January 26, 2019
- Trizol LS Reagent RNA Extraction Attempt • January 24, 2019
- Trizol LS Extraction - Qubit results show no detectable RNA • January 17, 2019
- First Attempts- Trying new BLAST +2.81 with new taxid options • January 15, 2019
- Error 3 on Centrifuge- Couldn't finish Extraction with TriZol LS Reagent • January 14, 2019
- 2015 Oysterseed DIA MSStats Figures Progress • January 7, 2019
- January 2019 Goals • January 1, 2019
2018
</ul>December 2018
- BLAST nt taxonomy with C bairdi had no taxonomy data • December 17, 2018
- Bioanalyzer Results - batch of cold, infected day 26 • December 14, 2018
- DIA analysis 2015 Cg seed continued • December 14, 2018
- 2015 C. gigas oysterseed DIA update • December 10, 2018
- DIA protocol, and Next Steps • December 7, 2018
- 2015 Oysterseed Plan and Crab Meeting Notes • December 6, 2018
November 2018
- Make Taxonomy Pie Charts in R • November 30, 2018
- Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line • November 26, 2018
- Cold, Infected Pool with RNeasy and DecaPod S1E13 • November 21, 2018
- RNeasy Test Bioanalyzer Results • November 16, 2018
- Submitted GSS poster, and my goals for Th and F • November 14, 2018
- BLASTn with Blue Crab and Prep for GSS Poster • November 13, 2018
- BLAST on Hummingbird and Transrate • November 12, 2018
- BLAST really running on Mox, 2015 Oysterseed new plan • November 8, 2018
- Sent BLAST to Mox, and Plan for rest of Week • November 6, 2018
- Trinity failed; Re-run, and Notes from Crab Meeting • November 1, 2018
- November Goals • November 1, 2018
October 2018
- BLAST with bad Trinity fasta, R plan for adding Qubit data, and Testing out RNeasy Plus Mirco Kit • October 31, 2018
- Re-run Trinity with correct files • October 30, 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
- Crab Project - try RNeasy Kit on some samples; Adding Qubit data to sample file • October 22, 2018
- RNA extraction and Running .fastq sequence files through FASTQC • October 19, 2018
- More Tri-reagent Extractions • October 10, 2018
- Plan for R and Bioanalyzer results • October 8, 2018
- Extract RNA from non-lyophilized C. bairdi hemolymph • October 5, 2018
- October Goals • October 5, 2018
September 2018
- DecaPod Submitted to Apple, RNA Extraction plan for Mon/Tues • September 28, 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
- DecaPod Season 1 Ep 11 - Crab Mtg • September 7, 2018
- Crab Meeting • September 6, 2018
- September Goals • September 1, 2018
August 2018
- Re-tried Skyline DIA • August 31, 2018
- Reading and Goals for now until Sept. 25th • August 30, 2018
- Gave Pooled Sample to the NWGC for Library Prep and RNA-Seq! • August 23, 2018
- Speed Vac New Pool of 15 Samples • August 22, 2018
- New Hemolymp sample and Qubit file; New RNA-seq short-term plan • August 20, 2018
- Streamlining Processing of Adding Qubit data to Master file • August 17, 2018
- Crab RNA-Seq thoughts; Merging columns in R • August 16, 2018
- New Plan - Lyophilizer; DIA Github Issue • August 13, 2018
- Learning code to change Factors to numbers • August 2, 2018
- Hemolymph sampling and Qubit data spreadsheet; Samples for Sam to run RNeasy Mini Plus Kit • August 1, 2018
- August Goals • August 1, 2018
July 2018
- My Bioanalyzer and Sam's RNA Clean-up Kit and RNeasy Plus Mini Kit results • July 31, 2018
- Trying out RNA protocol with 6x original protocol's volumes of reagents • July 30, 2018
- Skyline DIA with new BLIB made using Walnut • July 27, 2018
- Trying out Walnut; Crab Pool Update • July 26, 2018
- Crab Pools and Skyline Update • July 18, 2018
- Speed Vac Pt. 1 + Testing Advancing Peak Picking in Skyline • July 17, 2018
- Making Pools for RNASeq, and working on an ultimate MASTER crab spreadsheet • July 13, 2018
- Notes from Crab Meeting • July 5, 2018
- New Crab Pooling Plan for RNA Seq • July 2, 2018
June 2018
- Learning more about Trinity and working with large data sets; Update on Skyline issue • June 26, 2018
- Reading up on Trinity and Interviewed Genevieve Johnson for DecaPod • June 21, 2018
- Still have high error rates in Skyline - posted my issue to the Skyline support page • June 20, 2018
- Update on Crab Pooling and Plan for next week-ish • June 19, 2018
- 2015 Oysterseed Skyline questions • June 12, 2018
- Re-visiting error rate in Skyline and figuring out the math in pooling samples for sequencing • June 8, 2018
- Hackweek Day 1 • June 4, 2018
- Samples for Sequencing • June 3, 2018
- June Goals • June 3, 2018
May 2018
- RNA isolations for warm day 12 and master data file organization • May 23, 2018
- Weekly Goals • May 22, 2018
- R and figuring out qPCR and DNA Qubit data • May 14, 2018
- Bioanalyzer and Pubathon • May 8, 2018
- May Goals • May 3, 2018
- Crab Meeting and Bioanalyzer • May 3, 2018
- RNA Isolation and Data organization using R • May 2, 2018
- RNA Isolations continued • May 1, 2018
April 2018
- RNA Isolation and DecaPod S1E6 • April 29, 2018
- RNA isolation and Data org • April 26, 2018
- Data Organization- info from Pam in excel • April 25, 2018
- RNA Isolation Update and Upcoming Goals • April 24, 2018
- RNA isolation, Qubit, DecaPod updates • April 20, 2018
- Weekly goals • April 15, 2018
- Crab Project Updates • April 10, 2018
- Qubit results and DecaPod episodes • April 6, 2018
- Crab Project Updates • April 5, 2018
- April Goals • April 5, 2018
- RNA Isolation, continued, and plan for tomorrow • April 4, 2018
- RNA Isolation continued • April 3, 2018
March 2018
- Crab RNA Isolation and DIA Oyster Updates • March 29, 2018
- RNA iso with new protocol • March 28, 2018
- RNA Isolation info from Sam - Updated RNA isolation protocol; Qubit • March 27, 2018
- Trying to understand error rate in Skyline and Running Qubit • March 26, 2018
- Isolating RNA and trying to check Skyline error rates • March 21, 2018
- Re-do DIA, thinking about error rate determination • March 14, 2018
- Input from Emma on DIA and RNA isolation starts! • March 13, 2018
- Updates on RNA iso; podcast; DIA • March 12, 2018
- Updates on Podcast, DIA, RNA isolation, and Crab data organization • March 9, 2018
- March Goals • March 8, 2018
- Crab sample organization and Podcast Audacity Workshop notes • March 2, 2018
- Crab Meeting • March 1, 2018
February 2018
- RNA isolation • February 28, 2018
- Moving forward with DIA and plan for RNA isolation • February 27, 2018
- Weekly wrap-up and goals for next week • February 23, 2018
- Thesis Proposal Writing Class • February 21, 2018
- Running Qubit for the first time, and continuing DIA analysis • February 20, 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 protocol and plan for tomorrow • February 13, 2018
- Preliminary picks for RNA isolation • February 12, 2018
- 2015 Oysterseed DIA meeting notes • February 8, 2018
- Podcast and RNA isolation next steps • February 6, 2018
- Podcast testing • February 5, 2018
- February Goals • February 5, 2018
January 2018
- RNA isolation prep and 2015 oysterseed DIA update • January 30, 2018
- Podcast thoughts and Crab hemoolymph samples • January 26, 2018
- Preliminary Crab Sample Selection for Seq • January 25, 2018
- qPCR Machine arrival and training and Crab data and DIA updates • January 23, 2018
- DIA Next Steps and Crab Data Spreadsheet • January 22, 2018
- Crab Hemolymph Data Sheets Received • January 19, 2018
- Finished Determining Error Rate for DIA • January 17, 2018
- Determining error rate for DIA 2015 Oysterseed • January 16, 2018
- 2015 Oysterseed DIA Analysis Update • January 12, 2018
2017
</ul>December 2017
- Processing Hemolymph • December 20, 2017