()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  () 2015Oysterseed (2) Assembly (1) BLAST (7) Bioanalyzer (8) Bioanalyzer (8) Bri-line (1) Crab (1) CrabMeeting (2) CrabMeeting (2) CrabMtg (1) Crabproject (4) Crabproject (4) DAVID (1) DESeq2 (1) DIA (28) DIA (28) DIApaper (2) DNA-free (1) DataOrg (1) DataOrganization (1) Dataorganization (1) Dataorganization (1) DecaPod (6) DecaPod (6) DecaPod; (1) EncyclopeDIA (1) FASTQC (1) GO-MWU (1) GO_MWU (1) GSS (2) GSS2019 (1) Genewiz (1) Goals (1) Hackweek (1) Kallisto (3) Lyophilizer (3) Lyophilizer (3) MSStats (2) MSstats (1) MonthlyGoals (3) MonthlyGoals (3) Mox (5) NWGC (1) Nanodrop (1) Oysterseed () PCSGA (1) Podcast (4) Podcast (4) Pooling (1) Pools (1) Pub-a-thon () Pubathon () Qubit (13) Qubit (13) R (8) R (8) REVIGO (1) RNA (1) RNASeq (3) RNASeq (3) RNAisolation (35) RNAisolation (35) RNAseq (1) RNeasy (9) RNeasyKit (1) Reading (1) Rscript (1) SRM (1) Sequencing (1) Skyline (5) Skyline (5) SpeedVac (1) SpeedVac (1) Tannercrab () Transrate (1) Trinity (4) TrizolLS (5) WSG-mtg (1) Walnut (1) Walnut (1) Zymo (6) ZymoRNA (1) bairdi (2) concentration (1) crabproject () egg-dev (2) geo-stripspawn (4) goals (1) goals (1) hemolymph () organization (2) protocol (1) qPCR (1) qubit (1) supernatant (2) updates (2) updates (2)

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

  ()

 2015Oysterseed (2)

2015 Oysterseed Plan and Crab Meeting Notes
November Goals

 Assembly (1)

Sent First Trinity Assembly Job to Mox!

 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 (8)

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
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
Crab Meeting and Bioanalyzer

 Bioanalyzer (8)

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
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
Crab Meeting and Bioanalyzer

 Bri-line (1)

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

 Crab (1)

New Plan - Lyophilizer; DIA Github Issue

 CrabMeeting (2)

Trinity failed; Re-run, and Notes from Crab Meeting
Crab Meeting

 CrabMeeting (2)

Trinity failed; Re-run, and Notes from Crab Meeting
Crab Meeting

 CrabMtg (1)

DNA-free, Qubit, and Bioanalyzer Plan; Kallisto work

 Crabproject (4)

Streamlining Processing of Adding Qubit data to Master file
Notes from Crab Meeting
Re-visiting error rate in Skyline and figuring out the math in pooling samples for sequencing
RNA Isolation Update and Upcoming Goals

 Crabproject (4)

Streamlining Processing of Adding Qubit data to Master file
Notes from Crab Meeting
Re-visiting error rate in Skyline and figuring out the math in pooling samples for sequencing
RNA Isolation Update and Upcoming Goals

 DAVID (1)

Oysterseed DIA - New Analyses and wrapping up paper

 DESeq2 (1)

GSS 2019 Preparations - Differential Expression between infected and uninfected

 DIA (28)

DIA 2015 Oysterseed Plan (finish by Apr 17)
2015 Oysterseed DIA MSStats Figures Progress
DIA analysis 2015 Cg seed continued
2015 C. gigas oysterseed DIA update
DIA protocol, and Next Steps
Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line
BLAST really running on Mox, 2015 Oysterseed new plan
Re-tried Skyline DIA
Reading and Goals for now until Sept. 25th
Skyline DIA with new BLIB made using Walnut
Still have high error rates in Skyline - posted my issue to the Skyline support page
2015 Oysterseed Skyline questions
May Goals
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
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
DIA Next Steps and Crab Data Spreadsheet
Finished Determining Error Rate for DIA
Determining error rate for DIA 2015 Oysterseed
2015 Oysterseed DIA Analysis Update

 DIA (28)

DIA 2015 Oysterseed Plan (finish by Apr 17)
2015 Oysterseed DIA MSStats Figures Progress
DIA analysis 2015 Cg seed continued
2015 C. gigas oysterseed DIA update
DIA protocol, and Next Steps
Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line
BLAST really running on Mox, 2015 Oysterseed new plan
Re-tried Skyline DIA
Reading and Goals for now until Sept. 25th
Skyline DIA with new BLIB made using Walnut
Still have high error rates in Skyline - posted my issue to the Skyline support page
2015 Oysterseed Skyline questions
May Goals
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
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
DIA Next Steps and Crab Data Spreadsheet
Finished Determining Error Rate for DIA
Determining error rate for DIA 2015 Oysterseed
2015 Oysterseed DIA Analysis Update

 DIApaper (2)

Bairdi RNA extractions- other methods to try; Plan for Week
2015 DIA Oysterseed Paper Progress

 DNA-free (1)

DNA-free, Qubit, and Bioanalyzer Plan; Kallisto work

 DataOrg (1)

RNA isolations for warm day 12 and master data file organization

 DataOrganization (1)

Data Organization- info from Pam in excel

 Dataorganization (1)

Learning code to change Factors to numbers

 Dataorganization (1)

Learning code to change Factors to numbers

 DecaPod (6)

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
Bioanalyzer and Pubathon
Weekly goals
Qubit results and DecaPod episodes

 DecaPod (6)

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
Bioanalyzer and Pubathon
Weekly goals
Qubit results and DecaPod episodes

 DecaPod; (1)

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

 GO-MWU (1)

Tried some more GO-MWU stuff - not great - switching gears

 GO_MWU (1)

Trying GO-MWU with 2019 crab data

 GSS (2)

Submitted GSS poster, and my goals for Th and F
BLASTn with Blue Crab and Prep for GSS Poster

 GSS2019 (1)

GSS 2019 Preparations - Differential Expression between infected and uninfected

 Genewiz (1)

Sent samples to Genewiz

 Goals (1)

October Goals

 Hackweek (1)

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 (3)

Samples in Lyophilizer got all over the place
Start Lyophilizing to test new RNA extraction protocol using Tri-reagent
Crab Meeting

 Lyophilizer (3)

Samples in Lyophilizer got all over the place
Start Lyophilizing to test new RNA extraction protocol using Tri-reagent
Crab Meeting

 MSStats (2)

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

 MSstats (1)

DIA analysis 2015 Cg seed continued

 MonthlyGoals (3)

August 2019 Goals
February Goals
September Goals

 MonthlyGoals (3)

August 2019 Goals
February Goals
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

 NWGC (1)

Submitted 6 pooled crab samples to NWGC for QC

 Nanodrop (1)

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

 Oysterseed ()

 PCSGA (1)

Crab Project - What I did for PCSGA 2019

 Podcast (4)

April Goals
Crab sample organization and Podcast Audacity Workshop notes
Podcast and RNA isolation next steps
Podcast testing

 Podcast (4)

April Goals
Crab sample organization and Podcast Audacity Workshop notes
Podcast and RNA isolation next steps
Podcast testing

 Pooling (1)

Update on Crab Pooling and Plan for next week-ish

 Pools (1)

New Crab Pooling Plan for RNA Seq

 Pub-a-thon ()

 Pubathon ()

 Qubit (13)

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 Isolations continued
RNA Isolation and DecaPod S1E6
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

 Qubit (13)

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 Isolations continued
RNA Isolation and DecaPod S1E6
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

 R (8)

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
Crab RNA-Seq thoughts; Merging columns in R
Making Pools for RNASeq, and working on an ultimate MASTER crab spreadsheet

 R (8)

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
Crab RNA-Seq thoughts; Merging columns in R
Making Pools for RNASeq, and working on an ultimate MASTER crab spreadsheet

 REVIGO (1)

Oysterseed DIA - New Analyses and wrapping up paper

 RNA (1)

6 pooled Crab RNA samples - unsuccessful concentration with Zymo RNA Clean and Concentrator Kit -5

 RNASeq (3)

Gave Pooled Sample to the NWGC for Library Prep and RNA-Seq!
New Hemolymp sample and Qubit file; New RNA-seq short-term plan
Trying out Walnut; Crab Pool Update

 RNASeq (3)

Gave Pooled Sample to the NWGC for Library Prep and RNA-Seq!
New Hemolymp sample and Qubit file; New RNA-seq short-term plan
Trying out Walnut; Crab Pool Update

 RNAisolation (35)

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
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
Weekly Goals
RNA iso with new protocol
Updates on Podcast, DIA, RNA isolation, and Crab data organization
Crab Meeting
RNA isolation
RNA isolation protocol testing and DIA analysis re-do
RNA isolation protocol and plan for tomorrow
Preliminary picks for RNA isolation
Preliminary Crab Sample Selection for Seq

 RNAisolation (35)

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
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
Weekly Goals
RNA iso with new protocol
Updates on Podcast, DIA, RNA isolation, and Crab data organization
Crab Meeting
RNA isolation
RNA isolation protocol testing and DIA analysis re-do
RNA isolation protocol and plan for tomorrow
Preliminary picks for RNA isolation
Preliminary Crab Sample Selection for Seq

 RNAseq (1)

Sent samples to Genewiz

 RNeasy (9)

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

 RNeasyKit (1)

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

 Rscript (1)

R and figuring out qPCR and DNA Qubit data

 SRM (1)

Reading and Goals for now until Sept. 25th

 Sequencing (1)

Samples for Sequencing

 Skyline (5)

2015 C. gigas oysterseed DIA update
Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line
Re-tried Skyline DIA
Crab Pools and Skyline Update
Speed Vac Pt. 1 + Testing Advancing Peak Picking in Skyline

 Skyline (5)

2015 C. gigas oysterseed DIA update
Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line
Re-tried Skyline DIA
Crab Pools and Skyline Update
Speed Vac Pt. 1 + Testing Advancing Peak Picking in Skyline

 SpeedVac (1)

Speed Vac New Pool of 15 Samples

 SpeedVac (1)

Speed Vac New Pool of 15 Samples

 Tannercrab ()

 Transrate (1)

BLAST on Hummingbird and Transrate

 Trinity (4)

Trinity failed; Re-run, and Notes from Crab Meeting
Re-run Trinity with correct files
Sent First Trinity Assembly Job to Mox!
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 (1)

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

 Walnut (1)

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

 Zymo (6)

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

 ZymoRNA (1)

Notes on protocol and plan for Crab Project extractions - use info from Sam's notebook posts

 bairdi (2)

2015 Oysterseed Plan and Crab Meeting Notes
November Goals

 concentration (1)

6 pooled Crab RNA samples - unsuccessful concentration with Zymo RNA Clean and Concentrator Kit -5

 crabproject ()

 egg-dev (2)

Geoduck Egg Development - 3 days later
Geoduck Egg Development Test at Taylor Hatchery

 geo-stripspawn (4)

Sampling for D-hinge development
Day 1 of Trial 2 of Geoduck Stripspawn experiment - KCl dose + duration
Day 2 Geoduck Stripspawn Project at Taylor - not great results
Day 1 Geoduck Stripspawn Project at Taylor Shellfish Hathcery - Quilcene, WA

 goals (1)

June Goals

 goals (1)

June Goals

 hemolymph ()

 organization (2)

RNA Isolation and Data organization using R
RNA isolation and Data org

 protocol (1)

2015 C. gigas oysterseed DIA update

 qPCR (1)

qPCR Machine arrival and training and Crab data and DIA updates

 qubit (1)

6 pooled Crab RNA samples - unsuccessful concentration with Zymo RNA Clean and Concentrator Kit -5

 supernatant (2)

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

 updates (2)

RNA isolation, Qubit, DecaPod updates
Crab Project Updates

 updates (2)

RNA isolation, Qubit, DecaPod updates
Crab Project Updates