January 2024 Goals

January 2024 goals and daily notebook entries.

Goals

Writing and manuscripts

  1. Full draft of dissertation proposal
  2. Write full methods and physiological results for Astrangia 2021 experiment
  3. Revise and resubmit Astrangia review manuscript
  4. ICRS apps?
  5. Comp sci fellowship app ?
  6. Submit URI Dean Fellowship app

Sample processing

  1. Send RNA for sequencing for AH HI 2023 project
  2. Initial cell counts for Astrangia 2021
    • Count 20 samples and see how variable they are after homogenizing 2x
  3. Extract Mcap dev timeseries samples

Data analysis

  1. Finish stats for Astrangia 2021 phys data
  2. Work on Astrangia 2021 DEG analysis
    • Redo mapping with bowtie
    • See if I can figure out why DESeq2 code is being weird and not showing me all of the options for comparisons (maybe talk to Zoe)
  3. Map and quantify Astrangia 2021 miRNAs

Daily log

January 2

  • Revised professional objectives statement for URI dean’s fellowship app
  • QC for AH re-extracted samples and general sample organization
  • Aquarium daily stuff
  • Worked a little on beyond gene expression paper

January 3

  • Trimming for smRNA and mRNA data w/ fastp
  • Lot of code for trimming and alignment with smRNAs and mRNAs but I feel I am making progress
  • Aquarium daily stuff, cleaned BT3/4 and fed corals from that tank
  • Edits for Dean’s fellowship app

January 4

  • Edits for Dean’s fellowship app
  • Sent draft materials for dean’s fellowship app to BES leadership
  • Lots of trimming and aligning - bowtie2 and flexbar hate me today
  • Labeled tubes for extractions tomorrow
  • Created conda env for mirdeep2 and miranda. Was able to run mirdeep2!!!!!!!!!

January 5

  • Extraction for 12 dev timeseries samples
  • QC for flexbar trimming
  • Testing of random things on hpc

January 7

  • More smRNA and mRNA Astrangia 2021 coding

January 8

  • some smRNA and mRNA coding–jobs are pending
  • Phys plotting and data analysis for Astrangia 2021; writing up methods and results
  • Writing up protocol for miRNA library prep

January 9

  • Grad student meeting
  • mirdeep2 ran successfully on test sample!
  • Looked at mirdeep2 results
  • Started running flexbar for 25 bp
  • Started running another iteration of mirdeep2 without Nematostella as a reference species

January 10

  • Did smRNA coding
  • Met w/ Ariana

January 11

  • Aquarium work
  • Met w/ Danielle and Hollie
  • Worked on IDP and smart goals

January 12

  • Daily aquarium stuff
  • Pulled AH samples to send for sequencing on Monday + printed docs
  • IDP + SMART goals
  • E5 ncRNA meeting
  • Made E5 deep dive repo on OSF
  • Mirdeep2 w/ cnidarian miRNAs
  • Lab meeting

January 14

  • Sam to bam for mRNAs
  • Calculating mapping % for bowtie w/ mRNAs

January 15

  • Gene count matrix for bowtie complete
  • Comparing matrices from bowtie and hisat2
  • DESeq2 tests with bowtie matrix

January 16

  • Ran mirdeep2 on another test sample
  • lncRNA filtering steps
  • Went over PeerJ proof and resubmitted
  • Reviewed Zoe proposal
  • Made packing label + prepped samples, will ship AH samples tomorrow
  • Aquarium daily stuff

January 17

  • Freezer inventory and organization w/ Zoe
  • Talked DESeq2 with Zoe
  • Coding various iterations of DESeq2
  • Seminar on spatial transcriptomics
  • Shipped AH samples!

January 18

  • DESeq2 coding
  • Hollie meeting
  • Copied Federica’s data to my folder on Andromeda

January 19

  • Meeting summary + response
  • Lab meeting
  • QC and trimming for Pacuta HI 2022 data
  • Running test mirdeep2 for 25bp trimmed sample

January 20

  • QC for Pacuta
  • Making manuscript plots for carb chem pacuta manuscript
  • Comparing mirdeep2 25 v 30bp outputs – decided to go with 30bp trimming for smRNAs
  • Writing methods for Pacuta HI 2022

January 21

  • Alignment+assembly for Pacuta data
  • Methods writing for Pacuta
  • Methods writing for histology
  • Cat collapse for smRNA
  • First pass at deseq2 with Pacuta data

January 22

  • Freezer inventory w/ Zoe
  • DESeq2 for Pacuta + making figures
  • Prepped smRNA sequences for mirdeep2
  • Started mirdeep2 running for 5 samples

January 23

  • Shipped corals to AZ
  • Worked on mirdeep2 output and running more samples
  • LOTS of mirdeep2
  • Looking into MFE calculations

January 24

  • Revising abstract, intro, conclusion, and figures for Astrangia lit review manuscript
  • Writing group meeting
  • mirdeep2 on more samples
  • Quantifying reads w/ mirdeep2 quantifier.pl module
  • Tried to figure out how to calculate MFE

January 25

  • Making temp plot for Astrangia 2021 data yay!
  • Daily aquarium stuff and cleaning
  • Freezer inventory w/ Zoe

January 26

  • Gabe’s defense
  • Worked on ICRS proposal
  • e5 meeting
  • Send Pacuta info to collaborators

January 28

  • Started functional enrichment analysis for Pacuta – ran into an error about Cstack limit

January 29

  • Tried to troubleshoot functional enrichment analysis but still same error
  • Hollie meeting
  • Made ppt for lab meeting tomorrow
  • Genohub requests submitted
  • Outlined parts of intro for ICRS proposal
  • Looked at protein info for dev time series
  • Wrote some methods for ICRS
  • Made flyer for Yaamini talk

January 30

  • Troubleshooting for functional enrichment goseq error
  • Lab meeting
  • Looking at mirdeep2 results from each sample, seeing miRNAs shared across samples
  • Script to concatenate, collapse, adjust and remove <17nts for all AST samples, regardless of treatment or timepoint
  • Looked into genome assembly stuff

January 31

  • Trying to figure out how to do the concatnate collapse script w/o errors
  • Looking into genome assembly info (specifically hicanu)
  • Evaluated ribofree expression from express compare
  • Read paper for jclub
  • Jclub
  • Meeting w/ Danielle and Chloe
  • Looked at genohub quotes
  • Attempted form things

January reflection

Let’s reflect on how I did with my goals for the month.

Writing and manuscripts

  1. Full draft of dissertation proposal - nope, still trying to flesh out 3rd chapter but have narrowed it down to 2 options
  2. Write full methods and physiological results for Astrangia 2021 experiment - methods done, still need to finish phys results
  3. Revise and resubmit Astrangia review manuscript - currently in revision, will likely resubmit to Marine Biology or Biology Letters
  4. ICRS apps - have a solid draft of ICRS grad fellowship app
  5. Comp sci fellowship app - decided not to apply
  6. Submit URI Dean Fellowship app - done!

Sample processing

  1. Send RNA for sequencing for AH HI 2023 project - done!
  2. Initial cell counts for Astrangia 2021 - not done
    • Count 20 samples and see how variable they are after homogenizing 2x
  3. Extract Mcap dev timeseries samples - not done, but did a lot of library prep reading

Data analysis

  1. Finish stats for Astrangia 2021 phys data - almost done, need carbs
  2. Work on Astrangia 2021 DEG analysis - worked out DEG issues, need to do functional analysis
    • Redo mapping with bowtie
    • See if I can figure out why DESeq2 code is being weird and not showing me all of the options for comparisons (maybe talk to Zoe)
  3. Map and quantify Astrangia 2021 miRNAs - completed per sample, now doing all R1 reads

Overall, pretty good month. I felt more intentional in how I was spending my time and it was helpful to have goals to refer to. I also took on more projects/work (eg Apul genome, Pacuta paper, e5 wgbs) so I need to focus my priorities over the next month.

Written on January 2, 2024