February 2024 Goals

February 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. Resubmit Astrangia review manuscript
  4. ICRS app - due Feb 15
  5. Finish methods for Pacuta HI 2022 paper
  6. Finish intro and methods for e5 ncRNA paper

Sample processing

  1. Complete Mcap dev timeseries extractions
  2. Library prep for miRNAs (8 samples)
  3. Library prep with ribofree (8 samples)
  4. Library prep for WGBS (27 samples)
  5. Carbs for DT samples

Data analysis

  1. Finish stats for Astrangia 2021 phys data
  2. Work on Astrangia 2021 DEG and functional enrichment analysis
  3. Map and quantify Astrangia 2021 miRNAs
  4. Run miranda
  5. Begin genome assembly for Apul

Daily log

February 1

  • Aquarium daily stuff
  • Cleaned BT 1/2 and corals
  • Lab organization
  • Took photos of slides and stage micrometer for Chloe
  • Started looking at Pico methyl-seq protocol
  • Worked on ICRS app + budget
  • Made ICRS figure

February 2

  • Trying other cat iterations for smRNA data
  • Editing e5 ncRNA intro and methods
  • Meeting w/ Yaamini and Zoe
  • e5 ncRNA meeting
  • Some work on ICRS methods + intro, figure edits
  • Yaamini seminar

February 4

  • Watched videos on Zymo Ribofree library prep and Pico Seq library prep
  • Modified collapsed file for mirdeep2
  • Started running mapping and mirdeep2 for all R1 concatenated/collapsed reads
  • Edits for astrangia review manuscript

February 5

  • ICRS application edits
  • Filled out establishment of committee form and sent to committee to sign - completed by all parties
  • Tip inventory w/ Zoe
  • Freezer inventory w/ Zoe
  • Tip and tube estimates for Feb
  • Minor edits on Pacuta methods
  • Steven confirmed re ICRS rec letter
  • Astrangia review manuscript edits
  • Started remaking fig 3 in Astrangia review manuscript

February 6

  • Looking at mirdeep2 output
  • Lab meeting
  • Meeting w/ Hollie and Ross re genome assembly
  • Got packages
  • Editing figures for Astrangia review manuscript
  • Read about Canu / canu code
  • Started running bam2fastq for long reads

February 7

  • Lab github issue for freezer clean out
  • Edited Astrangia review manuscript forever
  • Writing meeting
  • Aquarium work
  • Labeled tubes for extraction tomorrow
  • Edits to ICRS proposal

February 8

  • Extractions w/ 12 DT samples
  • Zoe RNA discussion
  • Started running Canu

February 9

  • Freezer inventory w/ Zoe
  • Edits for Astrangia review manuscript
  • e5 molecular mechanisms meeting
  • Labeled tubes for extraction tomorrow

February 10

  • Extractions w/ 7 DT samples - changed protocol so there was no beads during beating step and used 300uL as input instead of 500uL

February 12

  • Edits to ICRS proposal, mostly done
  • Made new ICRS figure
  • Facilitated Fundamentals of Diversity DIBP workshop
  • Met w/ Chloe
  • Looked into Canu output
  • Started running hifiasm for assembly

February 13

  • Read about half of Helgoe et al. 2024 bleaching paper
  • Wrote about some potential post-doc ideas
  • Edits to Pacuta manuscript
  • Edits to ICRS proposal
  • Made ICRS CV
  • Wrote some of ICRS cover letter
  • Starting running busco on canu assembly
  • Looked at busco results

February 14

  • Prepped for ribofree library prep tomorrow (set thermocycler, labeled tubes, located + prepped reagents)
  • ICRS edits
  • Lab meeting
  • Aquarium room stuff
  • Writing up protocol for ribofree
  • Freezer inventory w/ Zoe

February 15

  • Submitted ICRS app!
  • RiboFree library prep with 2 samples (M60 and M72) + QC on tapestation
  • Started to write up library prep protocol for miRNAs

February 16

  • Finished DEG analysis for AST 2021 (still need to make figures pretty)
  • Met w/ new undergrad + Zoe
  • Colloquium

February 19

  • Ribofree library prep with 2 samples (M60 and M72 again) – only changed number of PCR amplification cycles (from 11 to 15)
  • Adding bioxriv papers to Astrangia review manuscript

February 20

  • Little sick
  • Lab meeting, discussed bleaching paper
  • Tried to get hifiadapterfilt to work

February 21

  • Still kinda sick
  • Eye appointment
  • Dr appointment
  • Changed solutions for Zoe corals
  • Labeled tubes for extractions
  • Figuring out what samples to do for the rest of ribofree preps
  • Looking at miRNA library prep input amount
  • Tried different iterations of canu and purge dups for Apul genome assembly

February 22

  • Still a lil sick
  • Extraction w/ 18 DT samples (some new, some re-extractions)
  • Cleaned freezers
  • Checked invoices for AH
  • Read a little for e5 meeting

February 23

  • Read for e5 meeting
  • Thought/wrote more about UPR
  • e5 meeting
  • Wrote out some of pico methyl-seq protocol
  • Organized spreadsheets for pico library prep samples

February 25

  • Organized sample info for ribofree library prep tomorrow with 6 samples

February 26

  • hifiasm still running
  • Ribofree library prep with 6 samples
  • Running test sample for quantifier.pl mirdeep2

February 27

  • Collapsing smRNA reads in prep for quantification
  • Finished comments on AH Mcap 2021 manuscript
  • Writing meeting
  • Worked on Astrangia review edits, framing the story
  • Quantified Astrangia miRNAs for all samples
  • Comparing miRNA data in R
  • Creating thermocycler settings for miRNA library prep
  • Aquarium room stuff

February 28

  • Biweekly summary
  • Edits to Astrangia review manuscript
  • Remaking fig 4 for Astrangia review manuscript
  • Lab meeting
  • Short DIBP
  • Remade some figures for Astrangia review

February 29

  • miRNA library prep test w/ 2 samples + QC
  • Edits to Astrangia review
  • Molecular methods for DT manuscript
  • Programmed thermocycler for switchfree library prep
  • Wrote up part of switchfree protocol

February reflection

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

Writing and manuscripts

  1. Full draft of dissertation proposal - no, but plan to have a full draft by end of next week
  2. Write full methods and physiological results for Astrangia 2021 experiment - still need to finish phys results
  3. Resubmit Astrangia review manuscript - still in revision
  4. ICRS app - due Feb 15 - done!
  5. Finish methods for Pacuta HI 2022 paper - basically done
  6. Finish intro and methods for e5 ncRNA paper - intro mostly done

Sample processing

  1. Complete Mcap dev timeseries extractions - done? did all of the ones that I needed to do for the time being
  2. Library prep for miRNAs (8 samples) - in progress
  3. Library prep with ribofree (8 samples) - done!
  4. Library prep for WGBS (27 samples) - not done, reading about protocol. Will start in the next few weeks
  5. Carbs for DT samples - nope

Data analysis

  1. Finish stats for Astrangia 2021 phys data - nope
  2. Work on Astrangia 2021 DEG and functional enrichment analysis - DEG analysis done, need to do functional annotation
  3. Map and quantify Astrangia 2021 miRNAs - done!
  4. Run miranda - not done
  5. Begin genome assembly for Apul - ran canu, hifiasm running currently
Written on February 1, 2024