West Coast Green Crab Experiment Part 78
Early vs. late timepoints
December 2025 Goals
Week 10 of the quarter! Two more weeks of academic instruction before free-for-all time begins! It feels incorrect that we are here and yet here were are!!!!! Time to lay down like Syril.
West Coast Green Crab Experiment Part 77
Wrapping up PLSDAs and ASCAs
West Coast Green Crab Experiment Part 76
Transcriptome assembly
West Coast Green Crab Experiment Part 75
Supervised analyses
West Coast Green Crab Experiment Part 74
RNA-Seq analysis plan
West Coast Green Crab Experiment Part 73
More PCA explorations
West Coast Green Crab Experiment Part 72
PCA explorations
November 2025 Goals
West Coast Green Crab Experiment Part 71
QC for RNA-Seq data
Green Crab Experiment Part 51
Google Gemini for literature search launch pad
West Coast Green Crab Experiment Part 70
Adding demographic information to respirometry analysis
West Coast Green Crab Experiment Part 69
Adding demographic information to TTR analysis
Green Crab Experiment Part 50
Things I realized were missing when I was updating methods and results
Green Crab Experiment Part 49
Retooling individual analyses with ASCA
October 2025 Goals
Green Crab Experiment Part 48
Metabolite-lipid relationships with DIABLO
Green Crab Experiment Part 47
Combined metabolomics-lipidomics WCNA
Green Crab Experiment Part 46
Intergrating physiology data with WCNA
Green Crab Experiment Part 45
Adding dispersion analysis to perMANOVA
Green Crab Experiment Part 44
Minor revisions to TTR and respirometry analysis
September 2025 Goals
West Coast Green Crab Experiment Part 68
Pooling libraries
West Coast Green Crab Experiment Part 67
Re-prepping low-yield libraries
West Coast Green Crab Experiment Part 66
Continuing first round of library preparation
July 2025 Goals
Cold Acclimation Green Crab Experiment Part 45
Final reviewer comments
West Coast Green Crab Experiment Part 65
Optimizing RNA library preparation + continuing with samples
Cold Acclimation Green Crab Experiment Part 44
Investigating impact of demographic variables
West Coast Green Crab Experiment Part 64
Continuing RNA library preparation
West Coast Green Crab Experiment Part 63
RNA library preparation part 2
West Coast Green Crab Experiment Part 62
Continuing RNA extractions
Cold Acclimation Green Crab Experiment Part 43
A quick recap of things I’ve revised
West Coast Green Crab Experiment Part 61
RNA library preparation part 1
Cold Acclimation Green Crab Experiment Part 42
Analyzing Catlin’s data
Cold Acclimation Green Crab Experiment Part 41
Revising the water temperature analysis
April 2025 Goals
West Coast Green Crab Experiment Part 60
RNA extractions
Cold Acclimation Green Crab Experiment Part 40
Population comparison for MA and WA crabs
Cold Acclimation Green Crab Experiment Part 39
Revising modeling for 2024 and Julia experiments
Cold Acclimation Green Crab Experiment Part 38
Water temperatures for WA and Julia’s experiments
Cold Acclimation Green Crab Experiment Part 37
Continuing with Catlin’s crabs
Cold Acclimation Green Crab Experiment Part 36
Making figures for the manuscript
Cold Acclimation Green Crab Experiment Part 35
Revising WA TTR data
West Coast Green Crab Experiment Part 59
Samples for metabolomics and lipidomics
Cold Acclimation Green Crab Experiment Part 34
Finishing WA crabs and starting on Catlin’s crabs
March 2025 Goals
Cold Acclimation Green Crab Experiment Part 33
Re-genotyping MA crabs and finishing WA crabs
Hawaii Gigas Methylation Analysis Part 23
Revising figures and numbers in text
Cold Acclimation Green Crab Experiment Part 32
Re-genotyping MA crabs
Cold Acclimation Green Crab Experiment Part 31
Temperature conditions during the MA experiment
Cold Acclimation Green Crab Experiment Part 30
Hardy-Weinberg equilibrium for MA and WA populations
West Coast Green Crab Experiment Part 58
Re-analyzing Julia’s data
Cold Acclimation Green Crab Experiment Part 29
Preliminary WA TTR analysis with genotype
Cold Acclimation Green Crab Experiment Part 28
Revising the MA TTR analysis
Green Crab Experiment Part 43
Interpreting metabolomic and lipidomic WCNA correlations
Cold Acclimation Green Crab Experiment Part 27
WA genotyping + some MA troubleshooting (because of course)
Green Crab Experiment Part 42
Supplementing the metabolomics analysis
Cold Acclimation Green Crab Experiment Part 26
Finishing MA genotyping
December 2024 Goals
Cold Acclimation Green Crab Experiment Part 25
Returning to ACTUAL genotyping
Green Crab Experiment Part 41
Supplementing the lipidomics analysis
Cold Acclimation Green Crab Experiment Part 24
Returning to genotyping troubleshooting (Part 2)
Cold Acclimation Green Crab Experiment Part 23
Returning to genotyping troubleshooting
November 2024 Goals
Green Crab Experiment Part 40
Revising figures
Green Crab Experiment Part 39
Correlating WCNA modules
Green Crab Experiment Part 38
Integrating all analyses
Green Crab Experiment Part 37
Digging into enrichment data
October 2024 Goals
West Coast Green Crab Experiment Part 57
Linear mixed effects models for TTR
Green Crab Experiment Part 36
Pairwise metabolomics enrichment
Green Crab Experiment Part 35
Pairwise lipidomics enrichment
Green Crab Experiment Part 34
Lipidomics enrichment
Green Crab Experiment Part 33
Lipidomics WCNA
Killifish Hypoxia RRBS Part 31
Fixing DMR figures
Green Crab Experiment Part 32
Reworking lipidomics analysis
September 2024 Goals
Green Crab Experiment Part 31
(Somewhat) finalized metabolomics figures
Green Crab Experiment Part 30
(Somewhat) finalized pathway analysis methods
Green Crab Experiment Part 29
Refining a priori metabolomics analysis
Killifish Hypoxia RRBS Part 30
DMR figures
Cold Acclimation Green Crab Experiment Part 22
Analyzing WA crab TTR data
Killifish Hypoxia RRBS Part 29
BAT_correlating
Killifish Hypoxia RRBS Part 28
DMR-DEG overlaps
August 2024 Goals
Cold Acclimation Green Crab Experiment Part 21
Trying some lipid blanks standards
Cold Acclimation Green Crab Experiment Part 20
Experiment log: WA experiment
Cold Acclimation Green Crab Experiment Part 19
Developing a lipid assay
Cold Acclimation Green Crab Experiment Part 18
Experiment log: WA acclimation
Cold Acclimation Green Crab Experiment Part 17
Analyzing TTR data for MA crabs
Cold Acclimation Green Crab Experiment Part 16
Genotyping MA crabs (back in troubleshooting land)
Cold Acclimation Green Crab Experiment Part 15
Genotyping MA crabs (but now it’s hell)
Cold Acclimation Green Crab Experiment Part 14
Experiment log: WA crabs!
Cold Acclimation Green Crab Experiment Part 13
Experiment log: experiment week!
Cold Acclimation Green Crab Experiment Part 12
Genotyping MA crabs
Cold Acclimation Green Crab Experiment Part 11
Experiment log: Acclimation week
Killifish Hypoxia RRBS Part 27
Characterizing DMR locations
Killifish Hypoxia RRBS Part 26
General methylation landscape figure
Cold Acclimation Green Crab Experiment Part 10
We have experimental animals!
Cold Acclimation Green Crab Experiment Part 9
Testing the restriction digest
Cold Acclimation Green Crab Experiment Part 8
Temperature tweaks and setting up the cold room
Cold Acclimation Green Crab Experiment Part 7
PCR optimization
June 2024 Goals
Cold Acclimation Green Crab Experiment Part 6
Picking a restriction enzyme
Cold Acclimation Green Crab Experiment Part 5
Making it even colder
Cold Acclimation Green Crab Experiment Part 4
Testing new primers
West Coast Green Crab Experiment Part 56
Finishing genotyping
Cold Acclimation Green Crab Experiment Part 3
Checking on temperatures
Cold Acclimation Green Crab Experiment Part 2
Designing a restriction digest
Killifish Hypoxia RRBS Part 25
Characterizing the general methylation landscape with the new genome
Killifish Hypoxia RRBS Part 24
Returning to the killifish project (again)
Cold Acclimation Green Crab Experiment
Starting the 2024 experiments
West Coast Green Crab Experiment Part 55
Troubleshooting sample 72
West Coast Green Crab Experiment Part 54
Rerunning samples on a gel
West Coast Green Crab Experiment Part 53
Extraction, PCR, and gel for remaining crabs
West Coast Green Crab Experiment Part 52
Extraction, PCR, and gel for remaining crabs
West Coast Green Crab Experiment Part 51
Extraction, PCR, and gel for remaining crabs
West Coast Green Crab Experiment Part 50
Extraction, PCR, and gel to “redo” crabs
Green Crab Experiment Part 28
Investigating specific metabolite and lipid pathways
West Coast Green Crab Experiment Part 49
Continued layover in contamination station
West Coast Green Crab Experiment Part 48
Results from genotyping round 2
West Coast Green Crab Experiment Part 47
Contamination station round 3
West Coast Green Crab Experiment Part 46
PCR and gel for TTR crabs
April 2024 Goals
West Coast Green Crab Experiment Part 45
Extractions, PCR, and gel for TTR crabs
West Coast Green Crab Experiment Part 44
Extractions, PCR, and gel for TTR crabs
CEABiGR Part 16
Some notes
CEABiGR Part 15
Enrichment, enrichment
CEABiGR Part 14
Analyzing changes in the maximum number of transcripts expressed
CEABiGR Part 13
Counting DML in genes with a predominant isoform shift
March 2024 Goals
West Coast Green Crab Experiment Part 43
Extractions, PCR, and gel for TTR crabs
West Coast Green Crab Experiment Part 42
Extractions, PCR, and gel for TTR crabs
CEABiGR Part 12
Continuing gene activity analyses
West Coast Green Crab Experiment Part 41
Extractions, PCR, and gel for TTR crabs
West Coast Green Crab Experiment Part 40
Extractions, PCR, and gel for TTR crabs
West Coast Green Crab Experiment Part 39
PCR and gel for TTR crabs
CEABiGR Part 11
Predominant isoform shift model
West Coast Green Crab Experiment Part 37
Extractions, PCR, and gel for respirometry + TTR crabs
West Coast Green Crab Experiment Part 37
Extractions, PCR, and gel for respirometry + TTR crabs
West Coast Green Crab Experiment Part 36
Testing out new SMC primers
West Coast Green Crab Experiment Part 35
Testing out new SMC primers
Green Crab Experiment Part 27
GLM for respirometry data
West Coast Green Crab Experiment Part 34
Individual-level analyses
February 2024 Goals
Green Crab Experiment Part 26
Experimental design edits
West Coast Green Crab Experiment Part 33
A reason for decontamination station
Green Crab Experiment Part 25
Simplifying the demographic data analysis
West Coast Green Crab Experiment Part 32
Still at decontamination station
West Coast Green Crab Experiment Part 31
Moving past decontamination station (for now)
Green Crab Experiment Part 24
Revising analyses
January 2024 Goals
Green Crab Experiment Part 23
Preliminary lipidomics analysis
Green Crab Experiment Part 22
Functional metabolomics analysis
Green Crab Experiment Part 21
Multivariate metabolomics analysis
West Coast Green Crab Experiment Part 30
Revisiting genotypes
December 2023 Goals
West Coast Green Crab Experiment Part 29
Decontamination station (my least favorite stop on the extraction train)
Green Crab Experiment Part 20
Making a plan for metabolomics analysis
West Coast Green Crab Experiment Part 28
Extractions, PCR, and gel for respirometry + TTR crabs
West Coast Green Crab Experiment Part 27
Modifying respirometry analysis
November 2023 Goals
West Coast Green Crab Experiment Part 26
Incorporating genotype into performance assays
West Coast Green Crab Experiment Part 25
Genotyping respirometry crabs
West Coast Green Crab Experiment Part 24
Preliminary analyses for 2023 experiment
West Coast Green Crab Experiment Part 23
Re-doing extractions, PCR, and gel for respirometry crabs
West Coast Green Crab Experiment Part 22
Extractions, PCR, and gel with third set of respirometry crabs
West Coast Green Crab Experiment Part 21
Extractions, PCR, and gel with second set of respirometry crabs
West Coast Green Crab Experiment Part 20
Re-trying extractions, PCR, and gel
Green Crab Experiment Part 19
Revising respirometry analysis
West Coast Green Crab Experiment Part 19
Re-trying PCR
West Coast Green Crab Experiment Part 18
Starting chelex extractions for genotyping
Green Crab Experiment Part 18
Analyzing respirometry data (finally)
West Coast Green Crab Experiment Part 17
Treatment Days 44-49
West Coast Green Crab Experiment Part 16
Treatment Days 40-43
West Coast Green Crab Experiment Part 15
Treatment Days 33-39
August 2023 Goals
West Coast Green Crab Experiment Part 14
Treatment Days 27-31
West Coast Green Crab Experiment Part 13
Treatment Days 23-26
West Coast Green Crab Experiment Part 12
Treatment Days 21-22
West Coast Green Crab Experiment Part 11
Treatment Days 16-20
West Coast Green Crab Experiment Part 10
Treatment Days 14-15
West Coast Green Crab Experiment Part 9
Treatment Days 10-13
West Coast Green Crab Experiment Part 8
Treatment Days 7-9
West Coast Green Crab Experiment Part 7
Treatment Days 1-6
July 2023 Goals
West Coast Green Crab Experiment Part 6
Acclimation Day 4 and 5
West Coast Green Crab Experiment Part 5
Experiment is UNDERWAY
Hawaii Gigas Methylation Analysis Part 22
The final countdown (for the Hawaii paper)
West Coast Green Crab Experiment Part 4
Finalized facility set-up
June 2023 Goals
West Coast Green Crab Experiment Part 3
Starting facility set-up
Green Crab Experiment Part 17
Finishing the demographic data analysis
West Coast Green Crab Experiment Part 2
Experiment planning update!
May 2023 Goals

West Coast Green Crab Experiment
Waterproof labelling system (I hope)
CEABiGR Part 10
Polynomial terms in transcriptional noise analysis
Green Crab Experiment Part 16
Time-to-right analysis
Green Crab Experiment Part 15
Survival analysis
April 2023 Goals

CEABiGR Part 9
Transcriptional noise analysis
March 2023 Goals

Green Crab Experiment Part 14
Analyzing demographic data
December 2022 Goals

Killifish Hypoxia RRBS Part 23
Pathway analysis for RNA-Seq data
November 2022 Goals

Killifish Hypoxia RRBS Part 22
Global methylation differences by population
CEABiGR Part 8
Alternative splicing analyses
CEABiGR Part 7
Gene methylation and expression mixOmics
October 2022 Goals

CEABiGR Part 6
Correlating gene methylation and expression
Killifish Hypoxia RRBS Part 21
Continuing with the new genome
Killifish Hypoxia RRBS Part 20
Re-align to the new genome
September 2022 Goals

Green Crab Experiment Part 13
Temperature conditions within tanks
August 2022 Goals

Green Crab Experiment Part 12
Treatment Days 18 through 22
Green Crab Experiment Part 11
Treatment Days 15 through 17
Green Crab Experiment Part 10
Treatment Days 11 through 14
CEABiGR Part 5
Genomic locations of DML
Green Crab Experiment Part 9
Treatment Days 8 through 10
Green Crab Experiment Part 8
Treatment Days 5 through 7
Green Crab Experiment Part 7
Treatment Days 3 and 4
Green Crab Experiment Part 6
Treatment Days 1 and 2
Green Crab Experiment Part 5
Acclimation Day 5 and 6
Green Crab Experiment Part 4
Acclimation Day 3 and 4
July 2022 Goals

Green Crab Experiment Part 3
Acclimation Day 2
Green Crab Experiment Part 3
Final set up + Day 1!
Green Crab Experiment Part 2
Setting up the experimental facility
Killifish Hypoxia RRBS Part 19
Wrapping up the initial methylation analysis
Killifish Hypoxia RRBS Part 18
Digging into DMR
June 2022 Goals

Green Crab Experiment
Respirometry trial
Killifish Hypoxia RRBS Part 17
Removing L4 samples
Killifish Hypoxia RRBS Part 16
Methylation landscape information
Killifish Hypoxia RRBS Part 15
Revised DMR identification
CEABiGR Part 4
Gene expression variability analyses
Killifish Hypoxia RRBS Part 14
Revisiting DMR identification
Killifish Hypoxia RRBS Part 13
Messing around with DMR identification
CEABiGR Part 3
Methylation landscape analysis
Killifish Hypoxia RRBS Part 12
Identifying DMR
Killifish Hypoxia RRBS Part 11
Figuring out my BAT_overview issues
Killifish Hypoxia RRBS Part 10
Moving forward with summarizing methylation
May 2022 Goals

Killifish Hypoxia RRBS Part 9
General methylation landscape comparisons
Killifish Hypoxia RRBS Part 8
Methylation extraction results
Killifish Hypoxia RRBS Part 7
Extracting methylation information
CEABiGR Part 2
Trying to tune the sPLS
Killifish Hypoxia RRBS Part 6
Continuing sample alignment
April 2022 Goals

Killifish Hypoxia RRBS Part 5
Full sample alignment
CEABiGR
Exon methylation and expression
Killifish Hypoxia RRBS Part 4
Continuing mapping tests
Killifish Hypoxia RRBS Part 3
Mapping RRBS data
March 2022 Goals

Uploading Data to NCBI SRA
Documenting for posterity (because it’s an annoying process)
WGBS Analysis Part 37
Thinking about SNPs
Killifish Hypoxia RRBS Part 2
Trimming RRBS data
Killifish Hypoxia RRBS
Starting a new project!
February 2022 Goals

January 2022 Goals

November 2021 Goals

WGBS Analysis Part 36
Miscellaneous enrichment investigations
WGBS Analysis Part 35
Gene librarian for genes with DML associated with enriched GOterms
WGBS Analysis Part 34
Digging into enrichment results
Nematostella Care
Protocol for care during non-experimental time
October 2021 Goals
August 2021 Goals

WGBS Analysis Part 33
Addressing reading committee edits
WGBS Analysis Part 32
Miscellaneous analyses
July 2021 Goals

WGBS Analysis Part 31
Revising methylKit parameters
WGBS Analysis Part 30
Finishing up analyses and figures!
Hawaii Gigas Methylation Analysis Part 21
Trying topGO for GOterm enrichment
Hawaii Gigas Methylation Analysis Part 20
Figures and statistical analyses
Hawaii Gigas Methylation Analysis Part 19
Restarting functional annotation with blastx
June 2021 Goals

Hawaii Gigas Methylation Analysis Part 18
Functional annotation for new C. gigas genome
Hawaii Gigas Methylation Analysis Part 17
Trying DSS for DML identification
Hawaii Gigas Methylation Analysis Part 16
Reworking pH-DML
WGBS Analysis Part 29
Running randomization tests on mox
Hawaii Gigas Methylation Analysis Part 15
Investigating methylation data
Hawaii Gigas Methylation Analysis Part 14
Messing around with methylKit DML settings
WGBS Analysis Part 28
Working with BS-Snper SNPs
WGBS Analysis Part 27
Characterizing DML
WGBS Analysis Part 26
Characterizing general methylation landscape
Hawaii Gigas Methylation Analysis Part 13
Comparative analysis with methylKit
WGBS Analysis Part 25
Generating genome feature tracks
WGBS Analysis Part 24
Troubleshooting R Studio server session timeouts
May 2021 Goals

WGBS Analysis Part 23
methylKit with R Studio server on mox
WGBS Analysis Part 22
Running R scripts on mox (for real this time)
WGBS Analysis Part 21
Running R scripts on mox
WGBS Analysis Part 20
Preparing to R scripts on mox
WGBS Analysis Part 19
Separating female and indeterminate samples
WGBS Analysis Part 18
Testing base methylKit code
WGBS Analysis Part 17
Identifying SNPs with BS-Snper
Hawaii Gigas Methylation Analysis Part 12
Identifying SNPs
April 2021 Goals

Hawaii Gigas Methylation Analysis Part 11
Merging BAM files
WGBS Analysis Part 16
Reviewing revised alignments
Hawaii Gigas Methylation Analysis Part 10
Processing Roslin alignments
WGBS Analysis Part 14
Testing methylKit parameters
Hawaii Gigas Methylation Analysis Part 9
Preliminary DML identification
Hawaii Gigas Methylation Analysis Part 8
WGS resequencing quote
Hawaii Gigas Methylation Analysis Part 7
Preliminary methylation investigation
WGBS Analysis Part 14
Reviewing bismark output
Hawaii Gigas Methylation Analysis Part 6
Aligning to the new C. gigas genome
March 2021 Goals

Hawaii Gigas Methylation Analysis Part 5
Evaluating bismark output
WGBS Analysis Part 13
Starting bismark with Manchester data
Virginica Gonad DNA Extractions Part 14
Sending samples for sequencing
WGBS Analysis Part 12
Reviewing trimgalore output with multiqc
WGBS Analysis Part 11
trimgalore output and fastqc
WGBS Analysis Part 10
Analyzing the full dataset
February 2021 Goals

Hawaii Gigas Methylation Analysis Part 4
Reviewing second round of trimming
Hawaii Gigas Methylation Analysis Part 3
Revisiting trimming
Hawaii Gigas Methylation Analysis Part 2
Checking trimmed data and starting bismark
Hawaii Gigas Methylation Analysis
Trimming Hawaii data
January 2021 Goals

WGBS Analysis Part 9
Investigating methylation island characteristics
Virginica Gonad DNA Extractions Part 13
Final sperm sample extractions
Virginica Gonad DNA Extractions Part 12
Re-extracting low-yield sperm samples
Virginica Gonad DNA Extractions Part 11
Extracting DNA and RNA from sperm samples
Virginica Gonad DNA Extractions Part 10
Testing protocol for sperm samples
December 2020 Goals

MethCompare Part 29
Returning to contingency tests
Virginica Gonad DNA Extractions Part 9
Re-extracting female samples 16 and 35
MethCompare Part 28
General methylation calculations
Virginica Gonad DNA Extractions Part 8
Checking female DNA quality
Virginica Gonad DNA Extractions Part 7
Checking female RNA quality
Virginica Gonad DNA Extractions Part 6
Checking female DNA and RNA quality
November 2020 Goals
Read MoreVirginica Gonad DNA Extractions Part 5
Remaining female DNA and RNA extractions
Virginica Gonad DNA Extractions Part 4
Subsampling remaining female tissue
Virginica Gonad DNA Extractions Part 3
Tweaking Zymo MicroPrep Kit protocols
Virginica Gonad DNA Extractions Part 2
Yields from Zymo MicroPrep Kit test samples
Virginica Gonad DNA Extractions
Testing the Zymo MicroPrep Kit (again)
October 2020 Goals

MethCompare Part 27
Revisiting the manuscript
September 2020 Goals

Sperm DNA MBD Enrichment Day 11
Finishing ethanol precipitations
Sperm DNA MBD Enrichment Day 10
DNA elution and ethanol precipitation (again)
Sperm DNA MBD Enrichment Day 9
MBD-Biotin wash and binding (again) and ethanol precipitations
Sperm DNA MBD Enrichment Day 8
DNA elution and ethanol precipitation
Sperm DNA MBD Enrichment Day 7
MBD-Biotin wash and binding
WGBS Samples Part 7
Final quality check
Sperm DNA MBD Enrichment Day 6
Final shearing and quality checks
WGBS Samples Part 6
Ethanol precipitations
WGBS Samples Part 5
Checking samples on the BioAnalyzer
Sperm DNA MBD Enrichment Day 5
Continuing shearing and quality checks
August 2020 Goals

WGBS Samples Part 4
More planning for WGBS
MethCompare Part 26
DMC locations and cleaning up scripts
WGBS Samples Part 3
Planning for WGBS
Sperm DNA MBD Enrichment Day 4
Re-shearing DNA and checking quality
MethCompare Part 25
Small tasks to complete the manuscript
Sperm DNA MBD Enrichment Day 3
Another QC check before enrichment
Sperm DNA MBD Enrichment Day 2
Additional sample preparation
Sperm DNA MBD Enrichment
Prepping for C. virginica sperm MBD Enrichment
Gigas and Virginica Labwork Priorities
Plan of attack for the mountain of labwork
MethCompare Part 24
Another (and hopefully final) iteration of union bedgraph analyses
MethCompare Part 23
Calculating median percent methylation
July 2020 Goals

MethCompare Part 22
Checking stacked barplots and post-hoc tests
MethCompare Part 21
Refining multivariate and modeling approaches
MethCompare Part 20
Preliminary follow-up GLMs
MethCompare Part 19
Multivariate analysis for compositional data
MethCompare Part 18
Formatting individual sample information
MethCompare Part 17
Fixing characterization code and remaking barplots
June 2020 Goals

Proposed Gigas and Virginica Labwork
Retooling labwork plans
MethCompare Part 16
Genome features and running the CpG characterization pipeline (again)
MethCompare Part 15
Statistical comparisons for methods
MethCompare Part 14
Reworking flanking and intergenic regions
MethCompare Part 13
Revamping distribution plots and creating genome feature plots
MethCompare Part 12
Characterizing union bedgraphs
MethCompare Part 11
More feature tracks
MethCompare Part 10
Revisiting CpG distributions
May 2020 Goals

MethCompare Part 9
CpG distributions
MethCompare Part 8
Characterizing CpGs in 5x data
MethCompare Part 7
Small tasks for future analyses
MethCompare Part 6
Retroactively obtaining checksums
MethCompare Part 5
Characterizing full samples
MethCompare Part 4
Modifying the CpG characterization pipeline
MethCompare Part 3
Finalizing genome feature tracks
MethCompare Part 2
More genome feature tracks
April 2020 Goals

MethCompare Recap
Comparing methylation analysis methods for two coral species
March 2020 Goals

DML Analysis Part 46
Epigenetics reading group feedback!
DML Analysis Part 45
Addressing reviewer comments
Gigas and Virginica Comparison Part 4
Reframing my questions and making a poster
Gigas and Virginica Comparison Part 3
C. gigas vs. C. virginica: DML
Gigas and Virginica Comparison Part 2
C. gigas vs. C. virginica: general methylation landscapes
Gigas and Virginica Comparison
Comparing Crassostrea spp. methylation patterns
Gigas Broodstock RNA Extraction
C. gigas RNA and DNA extractions: Day 1
February 2020 Goals

Figuring Out ATAC-Seq
Looking at labwork and sequencing options
Gigas Labwork Plans
Gearing up for C. gigas labwork
Final Virginica Tasks
Tying up loose ends for the C. virginica gonad paper
January 2020 Goals

DML Analysis Part 44
My last (I promise) analyses
December 2019 Goals

DML Analysis Part 43
Revising manuscript figures
November 2019 Goals

WGBS Analysis Part 8
Adding GOslim annotations to genes
October 2019 Goals

DML Analysis Part 42
Addressing collaborator feedback
DML Analysis Part 41
One last set of analyses before dedicated writing
WGBS Analysis Part 7
Further DML annotations
WGBS Analysis Part 6
Preliminary data for PCSGA
WGBS Analysis Part 5
Finalizing the analysis pipeline
WGBS Analysis Part 4
Looking at preliminary DML
WGBS Analysis Part 3
Rerunning bismark and starting with methylKit
WGBS Analysis Part 2
Fixing my bismark script for Mox
September 2019 Goals

WGBS Analysis
Testing bismark parameters for WGBS data
DMG Analysis Part 4
Characterizing GOslim terms
DMG Analysis Part 3
Enrichment and description of differentially methylated genes
DMG Analysis Part 2
Identifying differentially methylated genes
DMG Analysis
Starting the differentially methylated gene analysis
DML Analysis Part 40
Revised gene description using GO-MWU information
DML Analysis Part 39
Gene enrichment with GO-MWU
August 2019 Goals

Ecology of Infectious Marine Diseases TA Recap
Things I did at FHL that were not my research
DML Analysis Part 38
Gene enrichment and description
DML Analysis Part 37
Gene annotation tables
DML Analysis Part 36
Reworking DMR
June 2019 Goals

DML Analysis Part 35
Finalizing C. virginica tracks and revisiting analyses
FROGER Recap
My recollections of the Functional Re-annotation of Oyster Genomes with Epigenetic Resources (FROGER)
DML Analysis Part 34
Even more troubleshooting with IGV
DML Analysis Part 33
Continued troubleshooting
SEAS Outreach at Jane Addams Middle School
Teaching students about oysters and ocean acidification
May 2019 Goals

DML Analysis Part 32
Revised finalized general methylation trends
DML Analysis Part 31
Finalized general methylation trends
DML Analysis Part 30
Refining general methylation trends
April 2019 Goals

DML Analysis Part 29
Describing general methylation trends
DML Analysis Part 28
Revisiting DML analyses
DML Analysis Part 27
Resolving DML and DMR visualization issues
DML Analysis Part 26
Visualizing DML and DMR
Sperm DNA Extractions Part 5
Requantifying C. virginica sperm DNA extractions
Sperm DNA Extractions Part 4
Finishing C. virginica sperm DNA extractions
March 2019 Goals

Sperm DNA Extractions Part 3
Continuing sperm DNA extractions
DML Analysis Part 25
DML-mRNA gene product information
DML Analysis Part 24
Some information I’ve missed
Sperm DNA Extractions Part 2
Isolating and quantifying C. virginica sperm DNA
Sperm DNA Extractions
Extracting DNA from C. virginica sperm samples
DML Analysis Part 23
DMR-mRNA gene product information
DML Analysis Part 22
Gene enrichment for mRNA overlaps
WGBS Samples Part 2
Continuing isopropanol precipitations
WGBS Samples
Preparing C. gigas DNA for WGBS
February 2019 Goals

DML Analysis Part 21
Examining sample clustering
DML Analysis Part 20
Proportion test results
DML Analysis Part 19
Overlaps with methylKit gene background
January 2019 Goals

MEPS Revisions Part 4
Using simper and new figures
MEPS Revisions Part 3
Final unconstrained and constrained ordinations
MEPS Revisions Part 2
Protein abundance and environmental data NMDS
DML Analysis Part 18
Flanking analysis for mRNA coding regions
MEPS Revisions Part 1
Revisiting NMDS for protein abundance data
DML Analysis Part 17
methylKit and bedtools with Mox samples
November 2018 Goals

DML Analysis Part 16
Mox update
DML Analysis Part 15
Preliminary bedtools analysis
DML Analysis Part 14
Tiling window analysis in methylKit
DML Analysis Part 13
Different mincov values in methylKit
DML Analysis Part 12
Running bismark on Mox
DML Analysis Part 11
Testing methylKit parameters
Gigas Broodstock DNA Extraction Part 9
Sample extraction: Day 2
DML Analysis Part 10
Testing bismark parameters
October 2018 Goals

Gigas Broodstock DNA Extraction Part 8
Sample extraction: Day 1
Gigas Broodstock DNA Extraction Part 7
Extraction plan for actual samples
DML Analysis Part 9
Gene Enrichment Results from compGO
DML Analysis Part 8
DML-mRNA Gene Enrichment Results
DML Analysis Part 7
DML-mRNA Gene Enrichment
DML Analysis Part 6
Blasting for Uniprot codes (again)
Gigas Broodstock DNA Extraction Part 6
Protocol test: Round 4
September 2018 Goals
T-24 days until classes…
Gigas Broodstock DNA Extraction Part 5
Plan for another protocol test
Outreach with Refugee Women's Alliance Camp
Microscopes and the Fish Collection
Outreach with Botanical Gardens Summer Camp
Teaching students about cryptobenthic reef fish!
Gigas Broodstock DNA Extraction Part 4
Protocol test: Round 3
Gigas Broodstock DNA Extraction Part 3
Protocol test: Round 2
Gigas Broodstock DNA Extraction Part 2
Testing the extraction protocol
Gigas Broodstock DNA Extraction
Today’s hilarious labwork fail
August 2018 Goals
The last month of this academic year :0
Mixed Effects Models Part 2
Assumptions and p-values
Mixed Effects Models
lmers and glmers
DML Analysis Part 5
Blasting for Uniprot codes
DML Analysis Part 4
flankBed 101
DML Analysis Part 3
Quantifying proportion of overlaps
DML Analysis Part 2
Understanding gene enrichment
DML Analysis
Finding overlaps between DMLs and other things
June 2018 Goals
Another month, another set of dreams
Remaining Analyses Part 23
Revised salinity data!
Gonad Methylation Analysis Part 18
Preparing for discoveries
Gonad Methylation Analysis Part 17
Note to self: Always double check things
Gonad Methylation Analysis Part 16
A new enchilada
Gonad Methylation Analysis Part 15
A revised enchilada
Remaining Analyses Part 22
Revising environmental data
Gonad Methylation Analysis Part 14
A spoiled enchilada
Gonad Methylation Analysis Part 13
The whole enchilada (but better this time)
Gonad Methylation Analysis Part 12
Reproducibility rodeo
Gonad Methylation Analysis Part 11
I am Jerry Gergich
Gonad Methylation Analysis Part 10
Visualizing bismark outputs
Gonad Methylation Analysis Part 9
The whole enchilada
Gonad Methylation Analysis Part 8
What are those?!
May 2018 Goals
The meme has evolved
In Situ Carbonate Chemistry Parameters
CCC: Carbonate Chemistry Calculations
Gonad Methylation Analysis Part 7
M&M: methylKit and MACAU
pH Unit Conversion and Averaging
Having pH in mV makes no sense
Gonad Methylation Analysis Part 6
The end of a pipeline test
Gonad Methylation Analysis Part 5
When the stars (and sequences) align
Gonad Methylation Analysis Part 4
Preparing a genome (and my brain)
Gonad Methylation Analysis Part 3
Quality: controlled
Gonad Methylation Analysis Part 2
Yaamini vs. Computers
Gonad Methylation Analysis
Time to analyze the C. virginica data
Averaging Total Alkalinity
I have water chemistry data!
Project Ideas
Things to do if I had infinite research money
April 2018 Goals
April showers = More writing hours
Remaining Analyses Part 21
The curious case of the catalase(s)
Larval Mortality Analysis
Do I have a story for my larval data?
Gonad Histology Update 4
Another classification revision
Gonad Histology Update 3
GLMs are neat
Gonad Histology Update 2
I think I understand classification better now
March 2018 Goals
[Insert something witty about March Madness]
Remaining Analyses Part 20
This series has (finally) come to an end
Remaining Analyses Part 19
Digital drawing board: Round 2
Remaining Analyses Part 18
My better figure wasn’t actually good
Remaining Analyses Part 17
I created a better figure!
Remaining Analyses Part 16
Tying up (more) loose ends
Reproductive Output Analyses
i.e. My grand return to RStudio
Outreach with North Cascades Institute
The many paths to school
SEAS Outreach at Robert Eagle Staff Middle School!
Taught sixth grade science today!
February 2018 Goals
Tryna make the most out of this short month
Virginica MBDSeq Day 4
Rinse and repeat
Virginica MBDSeq Day 3
Dynabeads are dynamite
Virginica MBDSeq Day 2
A fulfilling day of labwork!
Comments and Tags
I pimped out my notebook!
Virginica MBDSeq
All systems go on C. Virginica sequencing!
Gonad Histology Update
Histology is not an exact science
January 2018 Goals
I guess break is over…
Remaining Analyses Part 15
The growth data wasn’t very interesting
Remaining Analyses Part 14
I see the light
Remaining Analyses Part 13
Triple-nested for loops are not fun
Sequencing Protocol Thoughts
a.k.a. How to take a break from proteomics
December 2017 Goals

Environmental Data from Micah Part 2
The last bit of data!
Environmental Data Meeting Part 3
Yesterday’s meeting notes
Remaining Analyses Part 12
Some more regressions
Remaining Analyses Part 11
Connecting the dots
Remaining Analyses Part 10
Following through on my plan
Gonad Histology Check-in
Quick journey into Manchester world
Remaining Analyses Part 9
My final NMDS
Remaining Analyses Part 8
Visualizing environmental and biomarker data
Remaining Analyses Part 7
Column comparisons
Environmental Data from Micah
More data, more problems…?
Environmental Data Meeting Part 2
Some more information from Micah and Alex
Remaining Analyses Part 6
Looked into ROC curves
Remaining Analyses Part 5
I’ve got the power
Remaining Analyses Part 4
Investigating those bad samples
Lab Notebook Maintenance Part 2
All lab notebook links are now fixed
Environmental Data Meeting
Science doesn’t take a day off
Remaining Analyses Part 3
I have significant results?!
Remaining Analyses Part 2
Everything at the peptide level
Remaining Analyses
Squeezing every last bit of information out of my data
November 2017 Goals

Correlating Technical Replicates Part 10
The end of a saga
First Committee Meeting
a.k.a. An excuse to make mini apple pie cheesecakes
Correlating Technical Replicates Part 9
Better results?
Correlating Technical Replicates Part 8
Maybe I should have called this series “Troubleshooting”…
Correlating Technical Replicates Part 7
I finally have technical replication I kinda trust?!
Correlating Technical Replicates Part 6
Dead ends and new plans
Correlating Technical Replicates Part 5
Things DO get better! (Kind of)
Correlating Technical Replicates Part 4
Continuing the PRTC confusion
Correlating Technical Replicates Part 3
I tried doing something statistically impossible today
Correlating Technical Replicates Part 2
Step 1: R-squared Cutoffs
Correlating Technical Replicates
Are some transitions worse than others?
Reproducible SRM Analysis
R&R: Review and Reproduce
October 2017 Goals

Lab Notebook Maintenance
We interrupt your regularly scheduled lab notebook perusing for some maintenance.
SRM Analysis Part 8
One script, infinite boxplots
SRM Analysis Part 7
Another Skyline saga
SRM Analysis Part 6
Retracing my steps
SRM Analysis Part 5
Everything sucks.
SRM Analysis Part 4
R Help is Helpful
SRM Analysis Part 3
All aboard the NMDS Struggle Bus
SRM Analysis Part 2
…Everybody Everywhere
SRM Analysis
Clean up, clean up
September 2017 Goals
