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

 BLAST (7)

First Attempts- Trying new BLAST +2.81 with new taxid options
BLAST nt taxonomy with C bairdi had no taxonomy data
BLASTn with Blue Crab and Prep for GSS Poster
BLAST on Hummingbird and Transrate
BLAST really running on Mox, 2015 Oysterseed new plan
Sent BLAST to Mox, and Plan for rest of Week
BLAST with bad Trinity fasta, R plan for adding Qubit data, and Testing out RNeasy Plus Mirco Kit

 Bioanalyzer (10)

Still no clear RNA bands on Bioanalyzer; Also working to get diff. exp. for GSS
DNA-free, Qubit, and Bioanalyzer Plan; Kallisto work
Bairdi RNA - Bioanalyzer and Nanodrop, Begin analyses for GSS - Kallisto
Bioanalyzer Results - batch of cold, infected day 26
Make Taxonomy Pie Charts in R
RNeasy Test Bioanalyzer Results
Plan for R and Bioanalyzer results
My Bioanalyzer and Sam's RNA Clean-up Kit and RNeasy Plus Mini Kit results
Bioanalyzer and Pubathon
Crab Meeting and Bioanalyzer

 Briline (1)

Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line

 CrabMeeting (9)

DNA-free, Qubit, and Bioanalyzer Plan; Kallisto work
Crab Meeting Notes
2015 Oysterseed Plan and Crab Meeting Notes
Trinity failed; Re-run, and Notes from Crab Meeting
DecaPod Season 1 Ep 11 - Crab Mtg
Crab Meeting
Notes from Crab Meeting
Crab Meeting and Bioanalyzer
Crab Meeting

 DAVID (2)

Oysterseed DIA - trying to characterize list of detected proteins in relation to _C. gigas_ proteome
Oysterseed DIA - New Analyses and wrapping up paper

 DESeq2 (2)

Crab Analyses Progress
GSS 2019 Preparations - Differential Expression between infected and uninfected

 DIA (1)

Oyster Paper Updates

 DIAOyster (70)

February Goals
January Goals
December Goals
June 2020 Goals
New DEG list comparing temperature - annotation, enrichment; annotation of oyster differentially abundant protein list
April 2020 Goals
March 2020 Goals
February Goals
January 2020 Goals
April 2020 Goals
December 2019 Goals
November 2019 Goals
October 2019 Goals
Oysterseed DIA - trying to characterize list of detected proteins in relation to _C. gigas_ proteome
Oysterseed DIA - New Analyses and wrapping up paper
Oysterseed project progress; Data uploaded to PRIDE
September Goals
DIA Oysterseed Project - Finishing up Paper and cleaning up repo - in progress
June Goals
May Goals
More tables for 2015 _C. gigas_ seed
Bairdi RNA extractions- other methods to try; Plan for Week
Annotated Protein List from MS Stats with set thresholds... in progress
Re-do MS Stats; DIA 2015 Oyster Updates
April Goals
2015 DIA Oysterseed Paper Progress
DIA 2015 Oysterseed Plan (finish by Apr 17)
2nd Half of March goals
February Goals
2015 Oysterseed DIA MSStats Figures Progress
January 2019 Goals
DIA analysis 2015 Cg seed continued
2015 C. gigas oysterseed DIA update
DIA protocol, and Next Steps
2015 Oysterseed Plan and Crab Meeting Notes
Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line
BLAST really running on Mox, 2015 Oysterseed new plan
November Goals
October Goals
September Goals
Re-tried Skyline DIA
Reading and Goals for now until Sept. 25th
New Plan - Lyophilizer; DIA Github Issue
August Goals
Skyline DIA with new BLIB made using Walnut
Crab Pools and Skyline Update
Speed Vac Pt. 1 + Testing Advancing Peak Picking in Skyline
Learning more about Trinity and working with large data sets; Update on Skyline issue
Still have high error rates in Skyline - posted my issue to the Skyline support page
Update on Crab Pooling and Plan for next week-ish
2015 Oysterseed Skyline questions
Re-visiting error rate in Skyline and figuring out the math in pooling samples for sequencing
June Goals
May Goals
Crab RNA Isolation and DIA Oyster Updates
Trying to understand error rate in Skyline and Running Qubit
Isolating RNA and trying to check Skyline error rates
Re-do DIA, thinking about error rate determination
Input from Emma on DIA and RNA isolation starts!
Updates on RNA iso; podcast; DIA
Updates on Podcast, DIA, RNA isolation, and Crab data organization
Moving forward with DIA and plan for RNA isolation
Weekly wrap-up and goals for next week
Running Qubit for the first time, and continuing DIA analysis
RNA isolation protocol testing and DIA analysis re-do
RNA isolation, Podcast thoughts, and DIA protocol
2015 Oysterseed DIA meeting notes
RNA isolation prep and 2015 oysterseed DIA update
qPCR Machine arrival and training and Crab data and DIA updates
2015 Oysterseed DIA Analysis Update

 DataOrganization (11)

Organizing Crab Qubit results and RNA isolation data - in progress
Hackweek Day 2 - Crab data sheets
Learning code to change Factors to numbers
Hemolymph sampling and Qubit data spreadsheet; Samples for Sam to run RNeasy Mini Plus Kit
RNA isolations for warm day 12 and master data file organization
Weekly Goals
R and figuring out qPCR and DNA Qubit data
RNA Isolation and Data organization using R
RNA isolation and Data org
Data Organization- info from Pam in excel
DIA Next Steps and Crab Data Spreadsheet

 DecaPod (15)

Cold, Infected Pool with RNeasy and DecaPod S1E13
DecaPod Submitted to Apple, RNA Extraction plan for Mon/Tues
DecaPod Season 1 Ep 11 - Crab Mtg
Reading up on Trinity and Interviewed Genevieve Johnson for DecaPod
Update on Crab Pooling and Plan for next week-ish
Weekly Goals
Bioanalyzer and Pubathon
RNA Isolation and DecaPod S1E6
RNA isolation, Qubit, DecaPod updates
Weekly goals
Crab Project Updates
Qubit results and DecaPod episodes
April Goals
Crab RNA Isolation and DIA Oyster Updates
Updates on RNA iso; podcast; DIA

 EncyclopeDIA (1)

Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line

 FASTQC (1)

RNA extraction and Running .fastq sequence files through FASTQC

 GOMWU (2)

Tried some more GO-MWU stuff - not great - switching gears
Trying GO-MWU with 2019 crab data

 GSS (4)

GSS 2019 Preparations - Differential Expression between infected and uninfected
Bairdi RNA - Bioanalyzer and Nanodrop, Begin analyses for GSS - Kallisto
Submitted GSS poster, and my goals for Th and F
BLASTn with Blue Crab and Prep for GSS Poster

 Genewiz (1)

Sent samples to Genewiz

 GeoduckStripSpawn (7)

Sampling for D-hinge development
Day 1 of Trial 2 of Geoduck Stripspawn experiment - KCl dose + duration
Geoduck Egg Development - 3 days later
Geoduck Egg Development Test at Taylor Hatchery
June Goals
Day 2 Geoduck Stripspawn Project at Taylor - not great results
Day 1 Geoduck Stripspawn Project at Taylor Shellfish Hathcery - Quilcene, WA

 Hackweek (2)

Hackweek Day 2 - Crab data sheets
Hackweek Day 1

 Kallisto (3)

Still no clear RNA bands on Bioanalyzer; Also working to get diff. exp. for GSS
DNA-free, Qubit, and Bioanalyzer Plan; Kallisto work
Bairdi RNA - Bioanalyzer and Nanodrop, Begin analyses for GSS - Kallisto

 Lyophilizer (4)

Samples in Lyophilizer got all over the place
Start Lyophilizing to test new RNA extraction protocol using Tri-reagent
Crab Meeting
New Plan - Lyophilizer; DIA Github Issue

 MSStats (2)

Re-do MS Stats; DIA 2015 Oyster Updates
2015 Oysterseed DIA MSStats Figures Progress

 MSstats (1)

DIA analysis 2015 Cg seed continued

 MonthlyGoals (1)

September Goals

 Mox (5)

BLAST really running on Mox, 2015 Oysterseed new plan
Sent BLAST to Mox, and Plan for rest of Week
Re-run Trinity with correct files
Sent First Trinity Assembly Job to Mox!
Worked more on R script for adding Qubit data; Started using Mox

 Nanodrop (1)

Bairdi RNA - Bioanalyzer and Nanodrop, Begin analyses for GSS - Kallisto

 OneHealth (1)

November 2019 Goals

 PCSGA (1)

Crab Project - What I did for PCSGA 2019

 PhD (10)

MUSP Day 18 through 26 Update and WAT Start and REX Start
MUSP Day 12 through 17 Update and Water Transmission (WAT) Prep and Pre-Filtering
MUSP Day 8 through 11 Update
August Goals
MUSP Day 6 and 7 Update
MUSP Day 1 through 5 Update
Start Multi-Species (MUSP) Experiment!!
Notes and Preparation for Multi-Species Experiment
Start Co-housing Multispecies - No disease exposure yet
I'm Back!! And Starting Grad School!! Again!!

 Pubathon (3)

2021 Pub-a-thon To-Dos and Progress
Bioanalyzer and Pubathon
May Goals

 Qubit (22)

6 pooled Crab RNA samples - unsuccessful concentration with Zymo RNA Clean and Concentrator Kit -5
More RNA extracted from Day 9 - RNA in all
Still no clear RNA bands on Bioanalyzer; Also working to get diff. exp. for GSS
DNA-free, Qubit, and Bioanalyzer Plan; Kallisto work
RNA extractions - more day 12 - RNA in 23 / 24
Second batch of 24 Crab hemolymph samples - RNA extracted and qubit results
Crab RNA extractions with Qubit results
Trying out RNA protocol with 6x original protocol's volumes of reagents
RNA Isolation and Data organization using R
RNA Isolations continued
RNA Isolation and DecaPod S1E6
RNA Isolation Update and Upcoming Goals
RNA isolation, Qubit, DecaPod updates
Weekly goals
Crab Project Updates
Qubit results and DecaPod episodes
April Goals
RNA Isolation, continued, and plan for tomorrow
RNA Isolation continued
RNA Isolation info from Sam - Updated RNA isolation protocol; Qubit
Trying to understand error rate in Skyline and Running Qubit
Running Qubit for the first time, and continuing DIA analysis

 R (11)

Make Taxonomy Pie Charts in R
BLAST with bad Trinity fasta, R plan for adding Qubit data, and Testing out RNeasy Plus Mirco Kit
Worked more on R script for adding Qubit data; Started using Mox
Crab Project - try RNeasy Kit on some samples; Adding Qubit data to sample file
Plan for R and Bioanalyzer results
New Hemolymp sample and Qubit file; New RNA-seq short-term plan
Streamlining Processing of Adding Qubit data to Master file
Crab RNA-Seq thoughts; Merging columns in R
Learning code to change Factors to numbers
Making Pools for RNASeq, and working on an ultimate MASTER crab spreadsheet
R and figuring out qPCR and DNA Qubit data

 REVIDO (1)

Oysterseed DIA - trying to characterize list of detected proteins in relation to _C. gigas_ proteome

 REVIGO (1)

Oysterseed DIA - New Analyses and wrapping up paper

 RNAIsolation (62)

Extract RNA from 24 samples - Day 9, 12 infected, 12 uninfected; still need to run on Qubit
More RNA extracted from Day 9 - RNA in all
Day 12, cold and warm, infected, uninfected RNA extractions - RNA in 24/24 samples
RNA extractions - more day 12 - RNA in 23 / 24
Day 12 RNA extractions - RNA in all samples!
Second batch of 24 Crab hemolymph samples - RNA extracted and qubit results
Crab RNA extractions with Qubit results
Notes on protocol and plan for Crab Project extractions - use info from Sam's notebook posts
Bairdi RNA extractions- other methods to try; Plan for Week
RNeasy Kit Extraction with 12 samples - RNA in 1/12
RNeasy Extraction Day 1 on 24 samples
Bairdi hemolymph extraction plan (work in progress)
RNeasy Kit Tube 516-2 starting sample testing
RNeasy Kit with hemo pellets using QIAshredder columns
Supernatant Trizol LS RNA Extraction attempt
Notes, Thoughts, and Ideas on RNA isolation (and thoughts from Sam)
Trizol LS Reagent RNA extraction using Geoduck hemolymph and oyster tissue
Qiagen RNeasy Micro Plus Kit with Geoduck hemolymph and oyster tissue
Trizol LS Reagent RNA Extraction Attempt
Trizol LS Extraction - Qubit results show no detectable RNA
Error 3 on Centrifuge- Couldn't finish Extraction with TriZol LS Reagent
BLAST with bad Trinity fasta, R plan for adding Qubit data, and Testing out RNeasy Plus Mirco Kit
Crab Project - try RNeasy Kit on some samples; Adding Qubit data to sample file
RNA extraction and Running .fastq sequence files through FASTQC
More Tri-reagent Extractions
Extract RNA from non-lyophilized C. bairdi hemolymph
DecaPod Submitted to Apple, RNA Extraction plan for Mon/Tues
Hemolymph sampling and Qubit data spreadsheet; Samples for Sam to run RNeasy Mini Plus Kit
August Goals
My Bioanalyzer and Sam's RNA Clean-up Kit and RNeasy Plus Mini Kit results
Trying out RNA protocol with 6x original protocol's volumes of reagents
RNA isolations for warm day 12 and master data file organization
Weekly Goals
RNA Isolation and Data organization using R
RNA Isolations continued
RNA Isolation and DecaPod S1E6
RNA isolation and Data org
RNA Isolation Update and Upcoming Goals
RNA isolation, Qubit, DecaPod updates
Weekly goals
Crab Project Updates
April Goals
RNA Isolation, continued, and plan for tomorrow
RNA Isolation continued
Crab RNA Isolation and DIA Oyster Updates
RNA iso with new protocol
RNA Isolation info from Sam - Updated RNA isolation protocol; Qubit
Trying to understand error rate in Skyline and Running Qubit
Isolating RNA and trying to check Skyline error rates
Input from Emma on DIA and RNA isolation starts!
Updates on RNA iso; podcast; DIA
Updates on Podcast, DIA, RNA isolation, and Crab data organization
Crab Meeting
RNA isolation
Moving forward with DIA and plan for RNA isolation
Weekly wrap-up and goals for next week
RNA isolation protocol testing and DIA analysis re-do
RNA isolation, Podcast thoughts, and DIA protocol
RNA isolation protocol and plan for tomorrow
Preliminary picks for RNA isolation
RNA isolation prep and 2015 oysterseed DIA update
Preliminary Crab Sample Selection for Seq

 RNeasy (10)

RNeasy Kit Extraction with 12 samples - RNA in 1/12
RNeasy Extraction Day 1 on 24 samples
Bairdi hemolymph extraction plan (work in progress)
RNeasy Kit Tube 516-2 starting sample testing
RNeasy Kit with hemo pellets using QIAshredder columns
RNeasy Plus Micro Kit Protocol using RNA Carrier and Supernatant
Qiagen RNeasy Micro Plus Kit with Geoduck hemolymph and oyster tissue
Cold, Infected Pool with RNeasy and DecaPod S1E13
BLAST with bad Trinity fasta, R plan for adding Qubit data, and Testing out RNeasy Plus Mirco Kit
Hemolymph sampling and Qubit data spreadsheet; Samples for Sam to run RNeasy Mini Plus Kit

 Reading (1)

Reading and Goals for now until Sept. 25th

 SRM (1)

Reading and Goals for now until Sept. 25th

 Sequencing (15)

Sent samples to Genewiz
Submitted 6 pooled crab samples to NWGC for QC
6 pooled Crab RNA samples - unsuccessful concentration with Zymo RNA Clean and Concentrator Kit -5
Attempt to concentrate test pools using Zymo RNA Clean and Concentrator Kit -5
Attempt at Concentrating Pooled (made from extra extracted RNA) Samples with the Zymo Microprep kit
Pooled 6 new samples for sequencing
Gave Pooled Sample to the NWGC for Library Prep and RNA-Seq!
New Hemolymp sample and Qubit file; New RNA-seq short-term plan
Crab RNA-Seq thoughts; Merging columns in R
Trying out Walnut; Crab Pool Update
Crab Pools and Skyline Update
Making Pools for RNASeq, and working on an ultimate MASTER crab spreadsheet
New Crab Pooling Plan for RNA Seq
Update on Crab Pooling and Plan for next week-ish
Samples for Sequencing

 Sequncing (1)

Closer to having some pooled libraries!

 Skyline (14)

2015 C. gigas oysterseed DIA update
Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line
September Goals
Re-tried Skyline DIA
New Plan - Lyophilizer; DIA Github Issue
Skyline DIA with new BLIB made using Walnut
Trying out Walnut; Crab Pool Update
Crab Pools and Skyline Update
Speed Vac Pt. 1 + Testing Advancing Peak Picking in Skyline
Re-do DIA, thinking about error rate determination
2015 Oysterseed DIA meeting notes
DIA Next Steps and Crab Data Spreadsheet
Finished Determining Error Rate for DIA
Determining error rate for DIA 2015 Oysterseed

 SpeedVac (2)

Speed Vac New Pool of 15 Samples
Speed Vac Pt. 1 + Testing Advancing Peak Picking in Skyline

 Supernatant (2)

Supernatant Trizol LS RNA Extraction attempt
RNeasy Plus Micro Kit Protocol using RNA Carrier and Supernatant

 Transrate (1)

BLAST on Hummingbird and Transrate

 Trinity (5)

Trinity failed; Re-run, and Notes from Crab Meeting
Re-run Trinity with correct files
Sent First Trinity Assembly Job to Mox!
Learning more about Trinity and working with large data sets; Update on Skyline issue
Reading up on Trinity and Interviewed Genevieve Johnson for DecaPod

 TrizolLS (5)

Supernatant Trizol LS RNA Extraction attempt
Trizol LS Reagent RNA extraction using Geoduck hemolymph and oyster tissue
Trizol LS Reagent RNA Extraction Attempt
Trizol LS Extraction - Qubit results show no detectable RNA
Error 3 on Centrifuge- Couldn't finish Extraction with TriZol LS Reagent

 WSG-mtg (1)

DIA 2015 Oysterseed Plan (finish by Apr 17)

 Walnut (3)

Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line
Skyline DIA with new BLIB made using Walnut
Trying out Walnut; Crab Pool Update

 Zymo (7)

More RNA extracted from Day 9 - RNA in all
Day 12, cold and warm, infected, uninfected RNA extractions - RNA in 24/24 samples
RNA extractions - more day 12 - RNA in 23 / 24
Day 12 RNA extractions - RNA in all samples!
Second batch of 24 Crab hemolymph samples - RNA extracted and qubit results
Crab RNA extractions with Qubit results
Notes on protocol and plan for Crab Project extractions - use info from Sam's notebook posts

 analyses (6)

Crab Analyses Progress
More Crab results - DESeq ABC v GHI; more heatmaps
Heatmap Practice
New DEG list comparing temperature - annotation, enrichment; annotation of oyster differentially abundant protein list
Submitted Thesis Chapters to Committee; Start working with New transcriptome
Annotate 2019 infection status DEG list; short-term paper plan

 bairdi (156)

February Goals
January Goals
December Goals
MS Thesis update
Crab Project Updates and Next Steps
Crab Analyses Progress
June 2020 Goals
More Crab results - DESeq ABC v GHI; more heatmaps
Heatmap Practice
New DEG list comparing temperature - annotation, enrichment; annotation of oyster differentially abundant protein list
Submitted Thesis Chapters to Committee; Start working with New transcriptome
Create annotated crab transcriptome BLAST `join` with uniprot SP GO
April 2020 Goals
Annotate 2019 infection status DEG list; short-term paper plan
Made new crab transcriptome stress response gene list; notes on crab immunity and macropinocytosis
Crab Results progress - GOslim transcriptome plot, macropinocytosis list and notes
Tried some more GO-MWU stuff - not great - switching gears
Trying GO-MWU with 2019 crab data
edgeR practice: crab 2019 data
March 2020 Goals
Create list of Trinity_IDs associated with GOslim "Stress response" from annotated crab transcriptome
Sent samples to Genewiz
February Goals
Submitted 6 pooled crab samples to NWGC for QC
Extract RNA from 24 samples - Day 9, 12 infected, 12 uninfected; still need to run on Qubit
6 pooled Crab RNA samples - unsuccessful concentration with Zymo RNA Clean and Concentrator Kit -5
Attempt to concentrate test pools using Zymo RNA Clean and Concentrator Kit -5
January 2020 Goals
April 2020 Goals
Attempt at Concentrating Pooled (made from extra extracted RNA) Samples with the Zymo Microprep kit
December 2019 Goals
Pooled 6 new samples for sequencing
More RNA extracted from Day 9 - RNA in all
GSS 2019 Preparations - Differential Expression between infected and uninfected
Still no clear RNA bands on Bioanalyzer; Also working to get diff. exp. for GSS
DNA-free, Qubit, and Bioanalyzer Plan; Kallisto work
Bairdi RNA - Bioanalyzer and Nanodrop, Begin analyses for GSS - Kallisto
Day 12, cold and warm, infected, uninfected RNA extractions - RNA in 24/24 samples
November 2019 Goals
RNA extractions - more day 12 - RNA in 23 / 24
Day 12 RNA extractions - RNA in all samples!
Second batch of 24 Crab hemolymph samples - RNA extracted and qubit results
Crab RNA extractions with Qubit results
Notes on protocol and plan for Crab Project extractions - use info from Sam's notebook posts
October 2019 Goals
September Goals
Organizing Crab Qubit results and RNA isolation data - in progress
August 2019 Goals
Hackweek Day 2 - Crab data sheets
Crab Meeting Notes
Closer to having some pooled libraries!
May Goals
Bairdi RNA extractions- other methods to try; Plan for Week
RNeasy Kit Extraction with 12 samples - RNA in 1/12
April Goals
RNeasy Extraction Day 1 on 24 samples
Bairdi hemolymph extraction plan (work in progress)
2nd Half of March goals
RNeasy Kit Tube 516-2 starting sample testing
RNeasy Kit with hemo pellets using QIAshredder columns
Supernatant Trizol LS RNA Extraction attempt
RNeasy Plus Micro Kit Protocol using RNA Carrier and Supernatant
Notes, Thoughts, and Ideas on RNA isolation (and thoughts from Sam)
February Goals
Trizol LS Reagent RNA extraction using Geoduck hemolymph and oyster tissue
Qiagen RNeasy Micro Plus Kit with Geoduck hemolymph and oyster tissue
Trizol LS Reagent RNA Extraction Attempt
Trizol LS Extraction - Qubit results show no detectable RNA
First Attempts- Trying new BLAST +2.81 with new taxid options
Error 3 on Centrifuge- Couldn't finish Extraction with TriZol LS Reagent
January 2019 Goals
BLAST nt taxonomy with C bairdi had no taxonomy data
Bioanalyzer Results - batch of cold, infected day 26
2015 Oysterseed Plan and Crab Meeting Notes
Make Taxonomy Pie Charts in R
Cold, Infected Pool with RNeasy and DecaPod S1E13
RNeasy Test Bioanalyzer Results
Submitted GSS poster, and my goals for Th and F
BLASTn with Blue Crab and Prep for GSS Poster
BLAST on Hummingbird and Transrate
BLAST really running on Mox, 2015 Oysterseed new plan
Sent BLAST to Mox, and Plan for rest of Week
Trinity failed; Re-run, and Notes from Crab Meeting
November Goals
BLAST with bad Trinity fasta, R plan for adding Qubit data, and Testing out RNeasy Plus Mirco Kit
Re-run Trinity with correct files
Sent First Trinity Assembly Job to Mox!
Worked more on R script for adding Qubit data; Started using Mox
Crab Project - try RNeasy Kit on some samples; Adding Qubit data to sample file
RNA extraction and Running .fastq sequence files through FASTQC
More Tri-reagent Extractions
Plan for R and Bioanalyzer results
Extract RNA from non-lyophilized C. bairdi hemolymph
October Goals
DecaPod Submitted to Apple, RNA Extraction plan for Mon/Tues
Samples in Lyophilizer got all over the place
Start Lyophilizing to test new RNA extraction protocol using Tri-reagent
DecaPod Season 1 Ep 11 - Crab Mtg
Crab Meeting
September Goals
Reading and Goals for now until Sept. 25th
Gave Pooled Sample to the NWGC for Library Prep and RNA-Seq!
Speed Vac New Pool of 15 Samples
New Hemolymp sample and Qubit file; New RNA-seq short-term plan
Streamlining Processing of Adding Qubit data to Master file
Crab RNA-Seq thoughts; Merging columns in R
Crab RNA-Seq thoughts; Merging columns in R
New Plan - Lyophilizer; DIA Github Issue
Learning code to change Factors to numbers
Hemolymph sampling and Qubit data spreadsheet; Samples for Sam to run RNeasy Mini Plus Kit
August Goals
My Bioanalyzer and Sam's RNA Clean-up Kit and RNeasy Plus Mini Kit results
Trying out RNA protocol with 6x original protocol's volumes of reagents
Trying out Walnut; Crab Pool Update
Crab Pools and Skyline Update
Speed Vac Pt. 1 + Testing Advancing Peak Picking in Skyline
Making Pools for RNASeq, and working on an ultimate MASTER crab spreadsheet
Notes from Crab Meeting
New Crab Pooling Plan for RNA Seq
Learning more about Trinity and working with large data sets; Update on Skyline issue
Reading up on Trinity and Interviewed Genevieve Johnson for DecaPod
Update on Crab Pooling and Plan for next week-ish
Re-visiting error rate in Skyline and figuring out the math in pooling samples for sequencing
June Goals
Weekly Goals
May Goals
Crab Meeting and Bioanalyzer
RNA Isolation and Data organization using R
RNA Isolations continued
RNA Isolation and DecaPod S1E6
RNA isolation and Data org
RNA Isolation Update and Upcoming Goals
RNA isolation, Qubit, DecaPod updates
Weekly goals
Qubit results and DecaPod episodes
Crab Project Updates
April Goals
RNA Isolation, continued, and plan for tomorrow
RNA Isolation continued
Crab RNA Isolation and DIA Oyster Updates
RNA iso with new protocol
RNA Isolation info from Sam - Updated RNA isolation protocol; Qubit
Trying to understand error rate in Skyline and Running Qubit
Isolating RNA and trying to check Skyline error rates
Input from Emma on DIA and RNA isolation starts!
Updates on RNA iso; podcast; DIA
Updates on Podcast, DIA, RNA isolation, and Crab data organization
Moving forward with DIA and plan for RNA isolation
Weekly wrap-up and goals for next week
Thesis Proposal Writing Class
Running Qubit for the first time, and continuing DIA analysis
RNA isolation protocol testing and DIA analysis re-do
RNA isolation, Podcast thoughts, and DIA protocol
Podcast and RNA isolation next steps
Podcast thoughts and Crab hemoolymph samples
qPCR Machine arrival and training and Crab data and DIA updates

 conferences (3)

January 2020 Goals
Crab Project - What I did for PCSGA 2019
August 2019 Goals

 dermasterias (9)

MUSP Day 18 through 26 Update and WAT Start and REX Start
MUSP Day 12 through 17 Update and Water Transmission (WAT) Prep and Pre-Filtering
MUSP Day 8 through 11 Update
August Goals
MUSP Day 6 and 7 Update
MUSP Day 1 through 5 Update
Start Multi-Species (MUSP) Experiment!!
Notes and Preparation for Multi-Species Experiment
Start Co-housing Multispecies - No disease exposure yet

 edgeR (1)

edgeR practice: crab 2019 data

 geoduck (5)

Sampling for D-hinge development
Day 1 of Trial 2 of Geoduck Stripspawn experiment - KCl dose + duration
Geoduck Egg Development - 3 days later
Geoduck Egg Development Test at Taylor Hatchery
Day 2 Geoduck Stripspawn Project at Taylor - not great results

 hemolymph (3)

RNA Isolation, continued, and plan for tomorrow
RNA Isolation continued
Processing Hemolymph

 histology (1)

Geoduck Slide Staging for Shelly

 paper (1)

Oyster Paper Updates

 pisaster (9)

MUSP Day 18 through 26 Update and WAT Start and REX Start
MUSP Day 12 through 17 Update and Water Transmission (WAT) Prep and Pre-Filtering
MUSP Day 8 through 11 Update
August Goals
MUSP Day 6 and 7 Update
MUSP Day 1 through 5 Update
Start Multi-Species (MUSP) Experiment!!
Notes and Preparation for Multi-Species Experiment
Start Co-housing Multispecies - No disease exposure yet

 podcast (6)

Updates on Podcast, DIA, RNA isolation, and Crab data organization
Crab sample organization and Podcast Audacity Workshop notes
RNA isolation, Podcast thoughts, and DIA protocol
Podcast and RNA isolation next steps
Podcast testing
Podcast thoughts and Crab hemoolymph samples

 pycnopodia (9)

MUSP Day 18 through 26 Update and WAT Start and REX Start
MUSP Day 12 through 17 Update and Water Transmission (WAT) Prep and Pre-Filtering
MUSP Day 8 through 11 Update
August Goals
MUSP Day 6 and 7 Update
MUSP Day 1 through 5 Update
Start Multi-Species (MUSP) Experiment!!
Notes and Preparation for Multi-Species Experiment
Start Co-housing Multispecies - No disease exposure yet

 pydnopodia (1)

I'm Back!! And Starting Grad School!! Again!!

 qPCR (1)

qPCR Machine arrival and training and Crab data and DIA updates

 staging (1)

Geoduck Slide Staging for Shelly

 thesis (9)

MS Thesis update
June 2020 Goals
Submitted Thesis Chapters to Committee; Start working with New transcriptome
April 2020 Goals
March 2020 Goals
February Goals
January 2020 Goals
November 2019 Goals
October 2019 Goals