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Lab Notebook by Yaamini Venkataraman

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West Coast Green Crab Experiment Part 63

RNA library preparation part 2

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West Coast Green Crab Experiment Part 62

Continuing RNA extractions

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Cold Acclimation Green Crab Experiment Part 43

A quick recap of things I’ve revised

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West Coast Green Crab Experiment Part 61

RNA library preparation part 1

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Cold Acclimation Green Crab Experiment Part 42

Analyzing Catlin’s data

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Cold Acclimation Green Crab Experiment Part 41

Revising the water temperature analysis

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March 2025 Goals

Image

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West Coast Green Crab Experiment Part 60

RNA extractions

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Cold Acclimation Green Crab Experiment Part 40

Population comparison for MA and WA crabs

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Cold Acclimation Green Crab Experiment Part 39

Revising modeling for 2024 and Julia experiments

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Cold Acclimation Green Crab Experiment Part 38

Water temperatures for WA and Julia’s experiments

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Cold Acclimation Green Crab Experiment Part 37

Continuing with Catlin’s crabs

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Cold Acclimation Green Crab Experiment Part 36

Making figures for the manuscript

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Cold Acclimation Green Crab Experiment Part 35

Revising WA TTR data

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West Coast Green Crab Experiment Part 59

Samples for metabolomics and lipidomics

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Cold Acclimation Green Crab Experiment Part 34

Finishing WA crabs and starting on Catlin’s crabs

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March 2025 Goals

Image

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Cold Acclimation Green Crab Experiment Part 33

Re-genotyping MA crabs and finishing WA crabs

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Hawaii Gigas Methylation Analysis Part 23

Revising figures and numbers in text

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Cold Acclimation Green Crab Experiment Part 32

Re-genotyping MA crabs

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Cold Acclimation Green Crab Experiment Part 31

Temperature conditions during the MA experiment

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Cold Acclimation Green Crab Experiment Part 30

Hardy-Weinberg equilibrium for MA and WA populations

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West Coast Green Crab Experiment Part 58

Re-analyzing Julia’s data

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Cold Acclimation Green Crab Experiment Part 29

Preliminary WA TTR analysis with genotype

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Cold Acclimation Green Crab Experiment Part 28

Revising the MA TTR analysis

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Green Crab Experiment Part 43

Interpreting metabolomic and lipidomic WCNA correlations

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Cold Acclimation Green Crab Experiment Part 27

WA genotyping + some MA troubleshooting (because of course)

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Green Crab Experiment Part 42

Supplementing the metabolomics analysis

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Cold Acclimation Green Crab Experiment Part 26

Finishing MA genotyping

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December 2024 Goals

Screen Shot 2022-08-05 at 11 08 00 AM

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Cold Acclimation Green Crab Experiment Part 25

Returning to ACTUAL genotyping

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Green Crab Experiment Part 41

Supplementing the lipidomics analysis

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Cold Acclimation Green Crab Experiment Part 24

Returning to genotyping troubleshooting (Part 2)

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Cold Acclimation Green Crab Experiment Part 23

Returning to genotyping troubleshooting

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November 2024 Goals

Screenshot 2024-10-14 at 9 43 36 AM

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Green Crab Experiment Part 40

Revising figures

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Green Crab Experiment Part 39

Correlating WCNA modules

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Green Crab Experiment Part 38

Integrating all analyses

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Green Crab Experiment Part 37

Digging into enrichment data

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October 2024 Goals

GXrx_oEbAAA-zLm

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West Coast Green Crab Experiment Part 57

Linear mixed effects models for TTR

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Green Crab Experiment Part 36

Pairwise metabolomics enrichment

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Green Crab Experiment Part 35

Pairwise lipidomics enrichment

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Green Crab Experiment Part 34

Lipidomics enrichment

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Green Crab Experiment Part 33

Lipidomics WCNA

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Killifish Hypoxia RRBS Part 31

Fixing DMR figures

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Green Crab Experiment Part 32

Reworking lipidomics analysis

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September 2024 Goals

FGsGrnGXEAAHKlx

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Green Crab Experiment Part 31

(Somewhat) finalized metabolomics figures

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Green Crab Experiment Part 30

(Somewhat) finalized pathway analysis methods

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Green Crab Experiment Part 29

Refining a priori metabolomics analysis

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Killifish Hypoxia RRBS Part 30

DMR figures

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Cold Acclimation Green Crab Experiment Part 22

Analyzing WA crab TTR data

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Killifish Hypoxia RRBS Part 29

BAT_correlating

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Killifish Hypoxia RRBS Part 28

DMR-DEG overlaps

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August 2024 Goals

Screenshot 2023-08-02 at 12 25 27 PM

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Cold Acclimation Green Crab Experiment Part 21

Trying some lipid blanks standards

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Cold Acclimation Green Crab Experiment Part 20

Experiment log: WA experiment

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Cold Acclimation Green Crab Experiment Part 19

Developing a lipid assay

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Cold Acclimation Green Crab Experiment Part 18

Experiment log: WA acclimation

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Cold Acclimation Green Crab Experiment Part 17

Analyzing TTR data for MA crabs

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Cold Acclimation Green Crab Experiment Part 16

Genotyping MA crabs (back in troubleshooting land)

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Cold Acclimation Green Crab Experiment Part 15

Genotyping MA crabs (but now it’s hell)

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Cold Acclimation Green Crab Experiment Part 14

Experiment log: WA crabs!

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Cold Acclimation Green Crab Experiment Part 13

Experiment log: experiment week!

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Cold Acclimation Green Crab Experiment Part 12

Genotyping MA crabs

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Cold Acclimation Green Crab Experiment Part 11

Experiment log: Acclimation week

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Killifish Hypoxia RRBS Part 27

Characterizing DMR locations

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Killifish Hypoxia RRBS Part 26

General methylation landscape figure

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Cold Acclimation Green Crab Experiment Part 10

We have experimental animals!

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Cold Acclimation Green Crab Experiment Part 9

Testing the restriction digest

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Cold Acclimation Green Crab Experiment Part 8

Temperature tweaks and setting up the cold room

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Cold Acclimation Green Crab Experiment Part 7

PCR optimization

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June 2024 Goals

Screenshot 2024-04-21 at 9 11 13 PM

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Cold Acclimation Green Crab Experiment Part 6

Picking a restriction enzyme

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Cold Acclimation Green Crab Experiment Part 5

Making it even colder

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Cold Acclimation Green Crab Experiment Part 4

Testing new primers

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West Coast Green Crab Experiment Part 56

Finishing genotyping

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Cold Acclimation Green Crab Experiment Part 3

Checking on temperatures

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Cold Acclimation Green Crab Experiment Part 2

Designing a restriction digest

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Killifish Hypoxia RRBS Part 25

Characterizing the general methylation landscape with the new genome

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Killifish Hypoxia RRBS Part 24

Returning to the killifish project (again)

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Cold Acclimation Green Crab Experiment

Starting the 2024 experiments

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West Coast Green Crab Experiment Part 55

Troubleshooting sample 72

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West Coast Green Crab Experiment Part 54

Rerunning samples on a gel

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West Coast Green Crab Experiment Part 53

Extraction, PCR, and gel for remaining crabs

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West Coast Green Crab Experiment Part 52

Extraction, PCR, and gel for remaining crabs

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West Coast Green Crab Experiment Part 51

Extraction, PCR, and gel for remaining crabs

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West Coast Green Crab Experiment Part 50

Extraction, PCR, and gel to “redo” crabs

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Green Crab Experiment Part 28

Investigating specific metabolite and lipid pathways

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West Coast Green Crab Experiment Part 49

Continued layover in contamination station

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West Coast Green Crab Experiment Part 48

Results from genotyping round 2

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West Coast Green Crab Experiment Part 47

Contamination station round 3

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West Coast Green Crab Experiment Part 46

PCR and gel for TTR crabs

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April 2024 Goals

FWQPpiyXgAAAqBl

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West Coast Green Crab Experiment Part 45

Extractions, PCR, and gel for TTR crabs

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West Coast Green Crab Experiment Part 44

Extractions, PCR, and gel for TTR crabs

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CEABiGR Part 16

Some notes

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CEABiGR Part 15

Enrichment, enrichment

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CEABiGR Part 14

Analyzing changes in the maximum number of transcripts expressed

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CEABiGR Part 13

Counting DML in genes with a predominant isoform shift

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March 2024 Goals

Screenshot 2024-02-28 at 10 55 23 AM

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West Coast Green Crab Experiment Part 43

Extractions, PCR, and gel for TTR crabs

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West Coast Green Crab Experiment Part 42

Extractions, PCR, and gel for TTR crabs

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CEABiGR Part 12

Continuing gene activity analyses

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West Coast Green Crab Experiment Part 41

Extractions, PCR, and gel for TTR crabs

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West Coast Green Crab Experiment Part 40

Extractions, PCR, and gel for TTR crabs

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West Coast Green Crab Experiment Part 39

PCR and gel for TTR crabs

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CEABiGR Part 11

Predominant isoform shift model

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West Coast Green Crab Experiment Part 37

Extractions, PCR, and gel for respirometry + TTR crabs

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West Coast Green Crab Experiment Part 37

Extractions, PCR, and gel for respirometry + TTR crabs

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West Coast Green Crab Experiment Part 36

Testing out new SMC primers

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West Coast Green Crab Experiment Part 35

Testing out new SMC primers

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Green Crab Experiment Part 27

GLM for respirometry data

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West Coast Green Crab Experiment Part 34

Individual-level analyses

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February 2024 Goals

Screenshot 2024-01-16 at 11 43 43 AM

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Green Crab Experiment Part 26

Experimental design edits

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West Coast Green Crab Experiment Part 33

A reason for decontamination station

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Green Crab Experiment Part 25

Simplifying the demographic data analysis

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West Coast Green Crab Experiment Part 32

Still at decontamination station

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West Coast Green Crab Experiment Part 31

Moving past decontamination station (for now)

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Green Crab Experiment Part 24

Revising analyses

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January 2024 Goals

Screen Shot 2022-10-18 at 10 29 14 AM

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Green Crab Experiment Part 23

Preliminary lipidomics analysis

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Green Crab Experiment Part 22

Functional metabolomics analysis

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Green Crab Experiment Part 21

Multivariate metabolomics analysis

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West Coast Green Crab Experiment Part 30

Revisiting genotypes

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December 2023 Goals

Ff5IhUhX0AEzcZz

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West Coast Green Crab Experiment Part 29

Decontamination station (my least favorite stop on the extraction train)

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Green Crab Experiment Part 20

Making a plan for metabolomics analysis

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West Coast Green Crab Experiment Part 28

Extractions, PCR, and gel for respirometry + TTR crabs

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West Coast Green Crab Experiment Part 27

Modifying respirometry analysis

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November 2023 Goals

Screenshot 2022-11-22 at 3 03 23 PM

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West Coast Green Crab Experiment Part 26

Incorporating genotype into performance assays

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West Coast Green Crab Experiment Part 25

Genotyping respirometry crabs

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West Coast Green Crab Experiment Part 24

Preliminary analyses for 2023 experiment

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West Coast Green Crab Experiment Part 23

Re-doing extractions, PCR, and gel for respirometry crabs

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West Coast Green Crab Experiment Part 22

Extractions, PCR, and gel with third set of respirometry crabs

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West Coast Green Crab Experiment Part 21

Extractions, PCR, and gel with second set of respirometry crabs

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West Coast Green Crab Experiment Part 20

Re-trying extractions, PCR, and gel

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Green Crab Experiment Part 19

Revising respirometry analysis

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West Coast Green Crab Experiment Part 19

Re-trying PCR

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West Coast Green Crab Experiment Part 18

Starting chelex extractions for genotyping

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Green Crab Experiment Part 18

Analyzing respirometry data (finally)

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West Coast Green Crab Experiment Part 17

Treatment Days 44-49

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West Coast Green Crab Experiment Part 16

Treatment Days 40-43

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West Coast Green Crab Experiment Part 15

Treatment Days 33-39

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August 2023 Goals

Screen Shot 2022-08-01 at 4 39 52 PM

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West Coast Green Crab Experiment Part 14

Treatment Days 27-31

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West Coast Green Crab Experiment Part 13

Treatment Days 23-26

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West Coast Green Crab Experiment Part 12

Treatment Days 21-22

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West Coast Green Crab Experiment Part 11

Treatment Days 16-20

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West Coast Green Crab Experiment Part 10

Treatment Days 14-15

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West Coast Green Crab Experiment Part 9

Treatment Days 10-13

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West Coast Green Crab Experiment Part 8

Treatment Days 7-9

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West Coast Green Crab Experiment Part 7

Treatment Days 1-6

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July 2023 Goals

Screenshot 2022-12-12 at 5 30 36 PM

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West Coast Green Crab Experiment Part 6

Acclimation Day 4 and 5

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West Coast Green Crab Experiment Part 5

Experiment is UNDERWAY

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Hawaii Gigas Methylation Analysis Part 22

The final countdown (for the Hawaii paper)

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West Coast Green Crab Experiment Part 4

Finalized facility set-up

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June 2023 Goals

FhsSG4MWAAAYzTT

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West Coast Green Crab Experiment Part 3

Starting facility set-up

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Green Crab Experiment Part 17

Finishing the demographic data analysis

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West Coast Green Crab Experiment Part 2

Experiment planning update!

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May 2023 Goals

FrqY5mqWcAIfAEl

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West Coast Green Crab Experiment

Waterproof labelling system (I hope)

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CEABiGR Part 10

Polynomial terms in transcriptional noise analysis

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Green Crab Experiment Part 16

Time-to-right analysis

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Green Crab Experiment Part 15

Survival analysis

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April 2023 Goals

Screenshot 2023-03-09 at 2 30 57 PM

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CEABiGR Part 9

Transcriptional noise analysis

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March 2023 Goals

Screenshot 2023-01-10 at 10 25 58 AM

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Green Crab Experiment Part 14

Analyzing demographic data

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December 2022 Goals

Fhq0cPSWQAEV-XH

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Killifish Hypoxia RRBS Part 23

Pathway analysis for RNA-Seq data

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November 2022 Goals

Screen Shot 2022-09-13 at 2 52 14 PM

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Killifish Hypoxia RRBS Part 22

Global methylation differences by population

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CEABiGR Part 8

Alternative splicing analyses

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CEABiGR Part 7

Gene methylation and expression mixOmics

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October 2022 Goals

life

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CEABiGR Part 6

Correlating gene methylation and expression

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Killifish Hypoxia RRBS Part 21

Continuing with the new genome

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Killifish Hypoxia RRBS Part 20

Re-align to the new genome

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September 2022 Goals

life

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Green Crab Experiment Part 13

Temperature conditions within tanks

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August 2022 Goals

life

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Green Crab Experiment Part 12

Treatment Days 18 through 22

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Green Crab Experiment Part 11

Treatment Days 15 through 17

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Green Crab Experiment Part 10

Treatment Days 11 through 14

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CEABiGR Part 5

Genomic locations of DML

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Green Crab Experiment Part 9

Treatment Days 8 through 10

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Green Crab Experiment Part 8

Treatment Days 5 through 7

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Green Crab Experiment Part 7

Treatment Days 3 and 4

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Green Crab Experiment Part 6

Treatment Days 1 and 2

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Green Crab Experiment Part 5

Acclimation Day 5 and 6

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Green Crab Experiment Part 4

Acclimation Day 3 and 4

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July 2022 Goals

life

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Green Crab Experiment Part 3

Acclimation Day 2

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Green Crab Experiment Part 3

Final set up + Day 1!

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Green Crab Experiment Part 2

Setting up the experimental facility

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Killifish Hypoxia RRBS Part 19

Wrapping up the initial methylation analysis

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Killifish Hypoxia RRBS Part 18

Digging into DMR

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June 2022 Goals

life

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Green Crab Experiment

Respirometry trial

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Killifish Hypoxia RRBS Part 17

Removing L4 samples

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Killifish Hypoxia RRBS Part 16

Methylation landscape information

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Killifish Hypoxia RRBS Part 15

Revised DMR identification

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CEABiGR Part 4

Gene expression variability analyses

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Killifish Hypoxia RRBS Part 14

Revisiting DMR identification

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Killifish Hypoxia RRBS Part 13

Messing around with DMR identification

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CEABiGR Part 3

Methylation landscape analysis

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Killifish Hypoxia RRBS Part 12

Identifying DMR

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Killifish Hypoxia RRBS Part 11

Figuring out my BAT_overview issues

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Killifish Hypoxia RRBS Part 10

Moving forward with summarizing methylation

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May 2022 Goals

life

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Killifish Hypoxia RRBS Part 9

General methylation landscape comparisons

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Killifish Hypoxia RRBS Part 8

Methylation extraction results

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Killifish Hypoxia RRBS Part 7

Extracting methylation information

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CEABiGR Part 2

Trying to tune the sPLS

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Killifish Hypoxia RRBS Part 6

Continuing sample alignment

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April 2022 Goals

life

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Killifish Hypoxia RRBS Part 5

Full sample alignment

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CEABiGR

Exon methylation and expression

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Killifish Hypoxia RRBS Part 4

Continuing mapping tests

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Killifish Hypoxia RRBS Part 3

Mapping RRBS data

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March 2022 Goals

life

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Uploading Data to NCBI SRA

Documenting for posterity (because it’s an annoying process)

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WGBS Analysis Part 37

Thinking about SNPs

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Killifish Hypoxia RRBS Part 2

Trimming RRBS data

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Killifish Hypoxia RRBS

Starting a new project!

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February 2022 Goals

life

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January 2022 Goals

image

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November 2021 Goals

Screen Shot 2021-06-09 at 12 57 59 PM

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WGBS Analysis Part 36

Miscellaneous enrichment investigations

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WGBS Analysis Part 35

Gene librarian for genes with DML associated with enriched GOterms

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WGBS Analysis Part 34

Digging into enrichment results

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Nematostella Care

Protocol for care during non-experimental time

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October 2021 Goals

gibbs

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August 2021 Goals

writing

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WGBS Analysis Part 33

Addressing reading committee edits

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WGBS Analysis Part 32

Miscellaneous analyses

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July 2021 Goals

post-defense

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WGBS Analysis Part 31

Revising methylKit parameters

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WGBS Analysis Part 30

Finishing up analyses and figures!

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Hawaii Gigas Methylation Analysis Part 21

Trying topGO for GOterm enrichment

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Hawaii Gigas Methylation Analysis Part 20

Figures and statistical analyses

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Hawaii Gigas Methylation Analysis Part 19

Restarting functional annotation with blastx

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June 2021 Goals

10things

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Hawaii Gigas Methylation Analysis Part 18

Functional annotation for new C. gigas genome

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Hawaii Gigas Methylation Analysis Part 17

Trying DSS for DML identification

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Hawaii Gigas Methylation Analysis Part 16

Reworking pH-DML

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WGBS Analysis Part 29

Running randomization tests on mox

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Hawaii Gigas Methylation Analysis Part 15

Investigating methylation data

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Hawaii Gigas Methylation Analysis Part 14

Messing around with methylKit DML settings

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WGBS Analysis Part 28

Working with BS-Snper SNPs

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WGBS Analysis Part 27

Characterizing DML

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WGBS Analysis Part 26

Characterizing general methylation landscape

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Hawaii Gigas Methylation Analysis Part 13

Comparative analysis with methylKit

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WGBS Analysis Part 25

Generating genome feature tracks

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WGBS Analysis Part 24

Troubleshooting R Studio server session timeouts

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May 2021 Goals

bob-ross

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WGBS Analysis Part 23

methylKit with R Studio server on mox

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WGBS Analysis Part 22

Running R scripts on mox (for real this time)

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WGBS Analysis Part 21

Running R scripts on mox

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WGBS Analysis Part 20

Preparing to R scripts on mox

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WGBS Analysis Part 19

Separating female and indeterminate samples

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WGBS Analysis Part 18

Testing base methylKit code

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WGBS Analysis Part 17

Identifying SNPs with BS-Snper

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Hawaii Gigas Methylation Analysis Part 12

Identifying SNPs

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April 2021 Goals

sorry-cake

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Hawaii Gigas Methylation Analysis Part 11

Merging BAM files

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WGBS Analysis Part 16

Reviewing revised alignments

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Hawaii Gigas Methylation Analysis Part 10

Processing Roslin alignments

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WGBS Analysis Part 14

Testing methylKit parameters

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Hawaii Gigas Methylation Analysis Part 9

Preliminary DML identification

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Hawaii Gigas Methylation Analysis Part 8

WGS resequencing quote

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Hawaii Gigas Methylation Analysis Part 7

Preliminary methylation investigation

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WGBS Analysis Part 14

Reviewing bismark output

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Hawaii Gigas Methylation Analysis Part 6

Aligning to the new C. gigas genome

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March 2021 Goals

yoda-tea

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Hawaii Gigas Methylation Analysis Part 5

Evaluating bismark output

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WGBS Analysis Part 13

Starting bismark with Manchester data

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Virginica Gonad DNA Extractions Part 14

Sending samples for sequencing

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WGBS Analysis Part 12

Reviewing trimgalore output with multiqc

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WGBS Analysis Part 11

trimgalore output and fastqc

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WGBS Analysis Part 10

Analyzing the full dataset

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February 2021 Goals

meow-meow

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Hawaii Gigas Methylation Analysis Part 4

Reviewing second round of trimming

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Hawaii Gigas Methylation Analysis Part 3

Revisiting trimming

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Hawaii Gigas Methylation Analysis Part 2

Checking trimmed data and starting bismark

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Hawaii Gigas Methylation Analysis

Trimming Hawaii data

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January 2021 Goals

130258807_10217771047444686_3780979396547541416_n

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WGBS Analysis Part 9

Investigating methylation island characteristics

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Virginica Gonad DNA Extractions Part 13

Final sperm sample extractions

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Virginica Gonad DNA Extractions Part 12

Re-extracting low-yield sperm samples

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Virginica Gonad DNA Extractions Part 11

Extracting DNA and RNA from sperm samples

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Virginica Gonad DNA Extractions Part 10

Testing protocol for sperm samples

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December 2020 Goals

124159023_10216466870736990_6760031238062394513_n

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MethCompare Part 29

Returning to contingency tests

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Virginica Gonad DNA Extractions Part 9

Re-extracting female samples 16 and 35

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MethCompare Part 28

General methylation calculations

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Virginica Gonad DNA Extractions Part 8

Checking female DNA quality

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Virginica Gonad DNA Extractions Part 7

Checking female RNA quality

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Virginica Gonad DNA Extractions Part 6

Checking female DNA and RNA quality

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November 2020 Goals

October Goals Recap

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Virginica Gonad DNA Extractions Part 5

Remaining female DNA and RNA extractions

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Virginica Gonad DNA Extractions Part 4

Subsampling remaining female tissue

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Virginica Gonad DNA Extractions Part 3

Tweaking Zymo MicroPrep Kit protocols

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Virginica Gonad DNA Extractions Part 2

Yields from Zymo MicroPrep Kit test samples

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Virginica Gonad DNA Extractions

Testing the Zymo MicroPrep Kit (again)

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October 2020 Goals

118652657_334056071047301_4165850583817331181_n

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MethCompare Part 27

Revisiting the manuscript

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September 2020 Goals

118510707_1214636152251845_508452252634736811_n

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Sperm DNA MBD Enrichment Day 11

Finishing ethanol precipitations

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Sperm DNA MBD Enrichment Day 10

DNA elution and ethanol precipitation (again)

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Sperm DNA MBD Enrichment Day 9

MBD-Biotin wash and binding (again) and ethanol precipitations

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Sperm DNA MBD Enrichment Day 8

DNA elution and ethanol precipitation

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Sperm DNA MBD Enrichment Day 7

MBD-Biotin wash and binding

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WGBS Samples Part 7

Final quality check

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Sperm DNA MBD Enrichment Day 6

Final shearing and quality checks

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WGBS Samples Part 6

Ethanol precipitations

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WGBS Samples Part 5

Checking samples on the BioAnalyzer

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Sperm DNA MBD Enrichment Day 5

Continuing shearing and quality checks

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August 2020 Goals

101719241_3090894984301898_8070696672528695296_o

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WGBS Samples Part 4

More planning for WGBS

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MethCompare Part 26

DMC locations and cleaning up scripts

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WGBS Samples Part 3

Planning for WGBS

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Sperm DNA MBD Enrichment Day 4

Re-shearing DNA and checking quality

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MethCompare Part 25

Small tasks to complete the manuscript

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Sperm DNA MBD Enrichment Day 3

Another QC check before enrichment

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Sperm DNA MBD Enrichment Day 2

Additional sample preparation

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Sperm DNA MBD Enrichment

Prepping for C. virginica sperm MBD Enrichment

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Gigas and Virginica Labwork Priorities

Plan of attack for the mountain of labwork

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MethCompare Part 24

Another (and hopefully final) iteration of union bedgraph analyses

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MethCompare Part 23

Calculating median percent methylation

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July 2020 Goals

EWeLmQlU4AET-ym

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MethCompare Part 22

Checking stacked barplots and post-hoc tests

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MethCompare Part 21

Refining multivariate and modeling approaches

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MethCompare Part 20

Preliminary follow-up GLMs

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MethCompare Part 19

Multivariate analysis for compositional data

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MethCompare Part 18

Formatting individual sample information

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MethCompare Part 17

Fixing characterization code and remaking barplots

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June 2020 Goals

FB_IMG_1590117749645

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Proposed Gigas and Virginica Labwork

Retooling labwork plans

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MethCompare Part 16

Genome features and running the CpG characterization pipeline (again)

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MethCompare Part 15

Statistical comparisons for methods

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MethCompare Part 14

Reworking flanking and intergenic regions

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MethCompare Part 13

Revamping distribution plots and creating genome feature plots

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MethCompare Part 12

Characterizing union bedgraphs

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MethCompare Part 11

More feature tracks

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MethCompare Part 10

Revisiting CpG distributions

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May 2020 Goals

92581126_3462108580471091_5583645690266910720_n

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MethCompare Part 9

CpG distributions

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MethCompare Part 8

Characterizing CpGs in 5x data

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MethCompare Part 7

Small tasks for future analyses

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MethCompare Part 6

Retroactively obtaining checksums

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MethCompare Part 5

Characterizing full samples

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MethCompare Part 4

Modifying the CpG characterization pipeline

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MethCompare Part 3

Finalizing genome feature tracks

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MethCompare Part 2

More genome feature tracks

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April 2020 Goals

Screen Shot 2020-04-03 at 12 55 00 PM

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MethCompare Recap

Comparing methylation analysis methods for two coral species

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March 2020 Goals

feels

Read More

DML Analysis Part 46

Epigenetics reading group feedback!

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DML Analysis Part 45

Addressing reviewer comments

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Gigas and Virginica Comparison Part 4

Reframing my questions and making a poster

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Gigas and Virginica Comparison Part 3

C. gigas vs. C. virginica: DML

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Gigas and Virginica Comparison Part 2

C. gigas vs. C. virginica: general methylation landscapes

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Gigas and Virginica Comparison

Comparing Crassostrea spp. methylation patterns

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Gigas Broodstock RNA Extraction

C. gigas RNA and DNA extractions: Day 1

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February 2020 Goals

feels

Read More

Figuring Out ATAC-Seq

Looking at labwork and sequencing options

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Gigas Labwork Plans

Gearing up for C. gigas labwork

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Final Virginica Tasks

Tying up loose ends for the C. virginica gonad paper

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January 2020 Goals

feels

Read More

DML Analysis Part 44

My last (I promise) analyses

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December 2019 Goals

feels

Read More

DML Analysis Part 43

Revising manuscript figures

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November 2019 Goals

feels

Read More

WGBS Analysis Part 8

Adding GOslim annotations to genes

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October 2019 Goals

feels

Read More

DML Analysis Part 42

Addressing collaborator feedback

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DML Analysis Part 41

One last set of analyses before dedicated writing

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WGBS Analysis Part 7

Further DML annotations

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WGBS Analysis Part 6

Preliminary data for PCSGA

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WGBS Analysis Part 5

Finalizing the analysis pipeline

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WGBS Analysis Part 4

Looking at preliminary DML

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WGBS Analysis Part 3

Rerunning bismark and starting with methylKit

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WGBS Analysis Part 2

Fixing my bismark script for Mox

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September 2019 Goals

feels

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WGBS Analysis

Testing bismark parameters for WGBS data

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DMG Analysis Part 4

Characterizing GOslim terms

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DMG Analysis Part 3

Enrichment and description of differentially methylated genes

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DMG Analysis Part 2

Identifying differentially methylated genes

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DMG Analysis

Starting the differentially methylated gene analysis

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DML Analysis Part 40

Revised gene description using GO-MWU information

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DML Analysis Part 39

Gene enrichment with GO-MWU

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August 2019 Goals

feels

Read More

Ecology of Infectious Marine Diseases TA Recap

Things I did at FHL that were not my research

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DML Analysis Part 38

Gene enrichment and description

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DML Analysis Part 37

Gene annotation tables

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DML Analysis Part 36

Reworking DMR

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June 2019 Goals

observe

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DML Analysis Part 35

Finalizing C. virginica tracks and revisiting analyses

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FROGER Recap

My recollections of the Functional Re-annotation of Oyster Genomes with Epigenetic Resources (FROGER)

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DML Analysis Part 34

Even more troubleshooting with IGV

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DML Analysis Part 33

Continued troubleshooting

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SEAS Outreach at Jane Addams Middle School

Teaching students about oysters and ocean acidification

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May 2019 Goals

Screen Shot 2019-04-28 at 1 18 16 PM

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DML Analysis Part 32

Revised finalized general methylation trends

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DML Analysis Part 31

Finalized general methylation trends

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DML Analysis Part 30

Refining general methylation trends

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April 2019 Goals

IMG_0173

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DML Analysis Part 29

Describing general methylation trends

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DML Analysis Part 28

Revisiting DML analyses

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DML Analysis Part 27

Resolving DML and DMR visualization issues

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DML Analysis Part 26

Visualizing DML and DMR

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Sperm DNA Extractions Part 5

Requantifying C. virginica sperm DNA extractions

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Sperm DNA Extractions Part 4

Finishing C. virginica sperm DNA extractions

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March 2019 Goals

fun

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Sperm DNA Extractions Part 3

Continuing sperm DNA extractions

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DML Analysis Part 25

DML-mRNA gene product information

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DML Analysis Part 24

Some information I’ve missed

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Sperm DNA Extractions Part 2

Isolating and quantifying C. virginica sperm DNA

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Sperm DNA Extractions

Extracting DNA from C. virginica sperm samples

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DML Analysis Part 23

DMR-mRNA gene product information

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DML Analysis Part 22

Gene enrichment for mRNA overlaps

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WGBS Samples Part 2

Continuing isopropanol precipitations

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WGBS Samples

Preparing C. gigas DNA for WGBS

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February 2019 Goals

fun

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DML Analysis Part 21

Examining sample clustering

Read More

DML Analysis Part 20

Proportion test results

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DML Analysis Part 19

Overlaps with methylKit gene background

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January 2019 Goals

fun

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MEPS Revisions Part 4

Using simper and new figures

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MEPS Revisions Part 3

Final unconstrained and constrained ordinations

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MEPS Revisions Part 2

Protein abundance and environmental data NMDS

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DML Analysis Part 18

Flanking analysis for mRNA coding regions

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MEPS Revisions Part 1

Revisiting NMDS for protein abundance data

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DML Analysis Part 17

methylKit and bedtools with Mox samples

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November 2018 Goals

fun

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DML Analysis Part 16

Mox update

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DML Analysis Part 15

Preliminary bedtools analysis

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DML Analysis Part 14

Tiling window analysis in methylKit

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DML Analysis Part 13

Different mincov values in methylKit

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DML Analysis Part 12

Running bismark on Mox

Read More

DML Analysis Part 11

Testing methylKit parameters

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Gigas Broodstock DNA Extraction Part 9

Sample extraction: Day 2

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DML Analysis Part 10

Testing bismark parameters

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October 2018 Goals

41859069_341442613097796_7325634397272691541_n

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Gigas Broodstock DNA Extraction Part 8

Sample extraction: Day 1

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Gigas Broodstock DNA Extraction Part 7

Extraction plan for actual samples

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DML Analysis Part 9

Gene Enrichment Results from compGO

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DML Analysis Part 8

DML-mRNA Gene Enrichment Results

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DML Analysis Part 7

DML-mRNA Gene Enrichment

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DML Analysis Part 6

Blasting for Uniprot codes (again)

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Gigas Broodstock DNA Extraction Part 6

Protocol test: Round 4

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September 2018 Goals

T-24 days until classes…

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Gigas Broodstock DNA Extraction Part 5

Plan for another protocol test

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Outreach with Refugee Women's Alliance Camp

Microscopes and the Fish Collection

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Outreach with Botanical Gardens Summer Camp

Teaching students about cryptobenthic reef fish!

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Gigas Broodstock DNA Extraction Part 4

Protocol test: Round 3

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Gigas Broodstock DNA Extraction Part 3

Protocol test: Round 2

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Gigas Broodstock DNA Extraction Part 2

Testing the extraction protocol

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Gigas Broodstock DNA Extraction

Today’s hilarious labwork fail

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August 2018 Goals

The last month of this academic year :0

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Mixed Effects Models Part 2

Assumptions and p-values

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Mixed Effects Models

lmers and glmers

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DML Analysis Part 5

Blasting for Uniprot codes

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DML Analysis Part 4

flankBed 101

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DML Analysis Part 3

Quantifying proportion of overlaps

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DML Analysis Part 2

Understanding gene enrichment

Read More

DML Analysis

Finding overlaps between DMLs and other things

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June 2018 Goals

Another month, another set of dreams

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Remaining Analyses Part 23

Revised salinity data!

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Gonad Methylation Analysis Part 18

Preparing for discoveries

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Gonad Methylation Analysis Part 17

Note to self: Always double check things

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Gonad Methylation Analysis Part 16

A new enchilada

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Gonad Methylation Analysis Part 15

A revised enchilada

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Remaining Analyses Part 22

Revising environmental data

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Gonad Methylation Analysis Part 14

A spoiled enchilada

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Gonad Methylation Analysis Part 13

The whole enchilada (but better this time)

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Gonad Methylation Analysis Part 12

Reproducibility rodeo

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Gonad Methylation Analysis Part 11

I am Jerry Gergich

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Gonad Methylation Analysis Part 10

Visualizing bismark outputs

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Gonad Methylation Analysis Part 9

The whole enchilada

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Gonad Methylation Analysis Part 8

What are those?!

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May 2018 Goals

The meme has evolved

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In Situ Carbonate Chemistry Parameters

CCC: Carbonate Chemistry Calculations

Read More

Gonad Methylation Analysis Part 7

M&M: methylKit and MACAU

Read More

pH Unit Conversion and Averaging

Having pH in mV makes no sense

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Gonad Methylation Analysis Part 6

The end of a pipeline test

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Gonad Methylation Analysis Part 5

When the stars (and sequences) align

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Gonad Methylation Analysis Part 4

Preparing a genome (and my brain)

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Gonad Methylation Analysis Part 3

Quality: controlled

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Gonad Methylation Analysis Part 2

Yaamini vs. Computers

Read More

Gonad Methylation Analysis

Time to analyze the C. virginica data

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Averaging Total Alkalinity

I have water chemistry data!

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Project Ideas

Things to do if I had infinite research money

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April 2018 Goals

April showers = More writing hours

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Remaining Analyses Part 21

The curious case of the catalase(s)

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Larval Mortality Analysis

Do I have a story for my larval data?

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Gonad Histology Update 4

Another classification revision

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Gonad Histology Update 3

GLMs are neat

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Gonad Histology Update 2

I think I understand classification better now

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March 2018 Goals

[Insert something witty about March Madness]

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Remaining Analyses Part 20

This series has (finally) come to an end

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Remaining Analyses Part 19

Digital drawing board: Round 2

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Remaining Analyses Part 18

My better figure wasn’t actually good

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Remaining Analyses Part 17

I created a better figure!

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Remaining Analyses Part 16

Tying up (more) loose ends

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Reproductive Output Analyses

i.e. My grand return to RStudio

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Outreach with North Cascades Institute

The many paths to school

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SEAS Outreach at Robert Eagle Staff Middle School!

Taught sixth grade science today!

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February 2018 Goals

Tryna make the most out of this short month

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Virginica MBDSeq Day 4

Rinse and repeat

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Virginica MBDSeq Day 3

Dynabeads are dynamite

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Virginica MBDSeq Day 2

A fulfilling day of labwork!

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Comments and Tags

I pimped out my notebook!

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Virginica MBDSeq

All systems go on C. Virginica sequencing!

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Gonad Histology Update

Histology is not an exact science

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January 2018 Goals

I guess break is over…

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Remaining Analyses Part 15

The growth data wasn’t very interesting

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Remaining Analyses Part 14

I see the light

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Remaining Analyses Part 13

Triple-nested for loops are not fun

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Sequencing Protocol Thoughts

a.k.a. How to take a break from proteomics

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December 2017 Goals

december-1st-meme-funny

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Environmental Data from Micah Part 2

The last bit of data!

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Environmental Data Meeting Part 3

Yesterday’s meeting notes

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Remaining Analyses Part 12

Some more regressions

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Remaining Analyses Part 11

Connecting the dots

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Remaining Analyses Part 10

Following through on my plan

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Gonad Histology Check-in

Quick journey into Manchester world

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Remaining Analyses Part 9

My final NMDS

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Remaining Analyses Part 8

Visualizing environmental and biomarker data

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Remaining Analyses Part 7

Column comparisons

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Environmental Data from Micah

More data, more problems…?

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Environmental Data Meeting Part 2

Some more information from Micah and Alex

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Remaining Analyses Part 6

Looked into ROC curves

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Remaining Analyses Part 5

I’ve got the power

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Remaining Analyses Part 4

Investigating those bad samples

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Lab Notebook Maintenance Part 2

All lab notebook links are now fixed

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Environmental Data Meeting

Science doesn’t take a day off

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Remaining Analyses Part 3

I have significant results?!

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Remaining Analyses Part 2

Everything at the peptide level

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Remaining Analyses

Squeezing every last bit of information out of my data

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November 2017 Goals

meme

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Correlating Technical Replicates Part 10

The end of a saga

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First Committee Meeting

a.k.a. An excuse to make mini apple pie cheesecakes

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Correlating Technical Replicates Part 9

Better results?

Read More

Correlating Technical Replicates Part 8

Maybe I should have called this series “Troubleshooting”…

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Correlating Technical Replicates Part 7

I finally have technical replication I kinda trust?!

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Correlating Technical Replicates Part 6

Dead ends and new plans

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Correlating Technical Replicates Part 5

Things DO get better! (Kind of)

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Correlating Technical Replicates Part 4

Continuing the PRTC confusion

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Correlating Technical Replicates Part 3

I tried doing something statistically impossible today

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Correlating Technical Replicates Part 2

Step 1: R-squared Cutoffs

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Correlating Technical Replicates

Are some transitions worse than others?

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Reproducible SRM Analysis

R&R: Review and Reproduce

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October 2017 Goals

screen shot 2017-10-02 at 1 39 40 pm

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Lab Notebook Maintenance

We interrupt your regularly scheduled lab notebook perusing for some maintenance.

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SRM Analysis Part 8

One script, infinite boxplots

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SRM Analysis Part 7

Another Skyline saga

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SRM Analysis Part 6

Retracing my steps

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SRM Analysis Part 5

Everything sucks.

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SRM Analysis Part 4

R Help is Helpful

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SRM Analysis Part 3

All aboard the NMDS Struggle Bus

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SRM Analysis Part 2

…Everybody Everywhere

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SRM Analysis

Clean up, clean up

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September 2017 Goals

3e2df6d28b149911e63f787fe14cb9dcfb607aeb6317a16e459d6bfa993bbfc2

Read More

Gigas Larvae Day 18

The end.

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Gigas Larvae Day 17

We have a Game Plan

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Gigas Larvae Day 16

The Final Countdown

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Gigas Larvae Day 15

They’re still not growing!

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Gigas Larvae Day 10

Checked the 80 micron screen again

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Gigas Larvae Day 9

Totes are pesky

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Gigas Larvae Day 8

Immersion heaters are pesky

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Gigas Larvae Day 7

Anoxia is no bueno

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Gigas Larvae Day 6

Smooth Saturday screening

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Gigas Larvae Day 5

Lots of maintenance today

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Gigas Larvae Day 4

My larvae are 60 microns now!

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Gigas Larvae Day 3

Counting larvae takes a while

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Gigas Larvae Day 2

A bit of a rough start today

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August 2017 Goals

I only have five goals

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Gigas Larvae Day 1

I’m the Mother of Oysters

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Gigas Larvae Day 0

Spoiler: We have baby oysters!

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Manchester Conditioning Update 11

NO OYSTERS DIED!

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Manchester Conditioning Update 10

It’s getting ugly

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Manchester Conditioning Update 9

The mortalities continue

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SRM Dilution Calculations 2

Revised for the last time

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SRM Dilution Calculations

My prior calculations were incorrect!

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Revised Spawning Plan

Featuring reduced crosses and pools

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Manchester Conditioning Update 8

Temperature is at 23 ºC!

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SRM Transition Protein Analysis

If you don’t have a visualization, did you really analyze data?

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SRM Assay Day 9

My samples are DONE.

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SRM Assay Day 8

Last day of my samples!

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SRM Assay Day 7

Status quo?

Read More

SRM Assay Day 6

Murphy’s Law is always relevant

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Manchester Conditioning Update 7

The power is back!

Read More

SRM Assay Day 5

Still plugging along

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Manchester Conditioning Update 6

Power outage edition

Read More

SRM Assay Day 3

More borrowed PRTC = All samples prepared

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SRM Assay Day 2

Our assay works!

Read More

SRM Assay Day 1

It’s SRM assay time!

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Selecting SRM Targets Part 7

WE HAVE OUR TARGETS.

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Selecting SRM Targets Part 6

Those peaks are running interference

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Manchester Conditioning Update 5

And the pH is low (again)

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Selecting SRM Targets Part 5

I have draft transitions!

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Selecting SRM Targets Part 4

Differential Expression + Protein Function = Targets?

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Manchester Conditioning Update 4

The pH is kind of stable?

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Selecting SRM Targets Part 3

MSstats works!

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July 2017 Goals

June was rather slow

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Preliminary Spawning Plan

It’s time to think about crosses!

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Manchester Conditioning Update 3

Revised (final?) Conditioning Plan

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Manchester Conditioning Update 2

Sophie’s New Choice: Temperature, Flow or pH?

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Manchester Conditioning Update

It’s been a slow burn

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Full Skyline Preliminary Analysis

I was gifted 3,000 extra proteins

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Skyline Error Checking Round 2

This time it only took 4 hours!

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Skyline Attempt 3

Remember that Skyline fail?

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Manchester Conditioning Plan

From Saturday 6/10 to Wednesday 7/5

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DNR Desalting Round 2

Last day of DNR extractions (hopefully)!

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Manchester Conditioning Setup

Time to fatten the oysters up!

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Manchester Heat Shock Experiment

It’s getting hot in here

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DNR Speed Vacuum Round 2

Yaamini vs. CentriVap: The Sequel

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June 2017 Goals

(Almost) done with Spring Quarter already?!

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DNR Mini Trypsin Digestion Round 3

I am now a faster pipetter

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DNR BCA Assay Round 3

All this protein but I’m still not swole.

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DNR Sample Preparation and Sonication Round 3

Here’s hoping this is the last round of DNR sample preparation!

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DNR Mini-Trypsin Digestion Round 2

I need to become a faster pipetter.

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DNR BCA Assay Round 2

We have lots of protein!

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DNR Sonication Round 2

How many times can you restart sample preparation?

Read More

DNR Sample Preparation Round 2

Slice and dice

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Protein Extractions Round 2, Part 2

More cowbell? More samples.

Read More

Another Skyline Fail

The DIA pipeline has been quite a #strugglebus

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Heat Shock Practice

It’s always good to practice your methods of torture.

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Skyline Error Checking

Who wants to manually quality check peptides?!

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Selecting SRM Targets Part 2

Record scratch. Freeze frame.

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Selecting SRM targets

Who are the lucky winners?

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Protein Extractions Round 2

It’s time to extract more protein.

Read More

Full Skyline Analysis

I can now analyze my full .blib!

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May 2017 Goals

It’s already MAY.

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Skyline Test 2

Skyline works with our demultiplexed files!

Read More

Downloading Metaanalysis Data

It’s not as easy as clicking a button

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Manchester Day 62

Laura went out to Manchester today and graciously cleaned my oysters

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Aggregating Metaanalysis Data

I became well-aquainted NCBI SRA database today

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Pubathon 14 Day Plan

I’m going to get stuff done for Pubathon (I promise)!

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Demultiplexing Update 3

My files are done converting!

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Demultiplexing Update 2

Another new MSConvert CLI

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Demultiplexing Update

New MSConvert CLI, hot off the presses

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Demultiplexing Data

Demultiplexing is perplexing

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Manchester Day 55

OA System Breakdown

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Manchester Day 52

We’re done with our OA experiment!

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April 2017 Goals

I was so busy catching up on classes I forgot it was April!

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Manchester Day 44

What happened when Laura got stranded in the Midwest

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Manchester Day 42

I’m at NSA, to Grace and Olivia went to Manchester.

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NSA Poster

Here’s the evolution of my poster for NSA!

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Manchester Day 36

Checking in before we leave for NSA

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Preliminary Data Analysis

On that number-crunching grind

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Skyline Test Run

We have data!!!

Read More

Manchester Day 26

A couple hiccups at Manchester today

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PECAN Update 5

It works!

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Manchester Data Log

Yesterday I set up a system for cataloging our water chemistry data.

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PECAN Update 4

Reformatting PECAN inputs

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PECAN Update 3

New day, same errors

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Manchester Day 21

We’re officially halfway through our pH treatment window!

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PECAN Update 2

To reconvert or not reconvert?

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PECAN Update 1

Hit an obstacle with PECAN this weekend.

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Manchester Day 19

Another smooth day at Manchester!

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PECAN Run 1

:cake: It’s not as easy as pie :cake:

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March 2017 Goals

March Maddness is upon us.

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Manchester Day 14

Today, I spent 3 hours cleaning oyster :poop:

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Manchester Day 12

The OA System is up and running!

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February 2017 Goals Update

February Goals Update

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Scientist in the Classroom

Conducted my first outreach activity today!

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Feb. 4 Manchester Sampling

First Manchester Sampling

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February 2017 Goals

February Goals

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Mass Spec Update 3

…But now trouble is gone!

Read More

Mass Spec Update

…And trouble stuck around at 3:51 p.m. on January 29.

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Mass Spec Updates

Trouble struck at 8:16 p.m. on January 28.

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Mass Spec Start

My samples are on the Mass Spec!

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Mass Spec Set-up

Mass Spectrometer Set-up

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MZ ratios

M/Z ratios: Mass hysteria ensues

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PRTC preparation

PRTC: We know what those peptides can be

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Desalting

Not Salty about Desalting

Read More

Speed Vacuum

Speed Vacuum = Slow Process

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Mini-Trypsin Digestion

Trippin for Trypsin

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BCA Assay Trial 2

If at first you don’t succeed, trial trial again.

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BCA Assay Trial 1

Practice makes perfect?

Read More

Sonication

Gill Tissue + Sound Waves = Protein Soup

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Preparing for Protein Extractions

My first day in lab was a busy one!

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December 2016 Goals

My DNR project is still on the brain!.

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November 2016 Goals

Now that it’s almost November, it’s time to get cracking on the DNR project.

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Collaboration with the Department of Natural Resources

As promised, here is some background on my current project

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An Introduction

Hello!

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