March 2024 Goals

March 2024 goals and daily notebook entries.

Goals

Writing and manuscripts

Full draft of dissertation proposal
Write physiological results for Astrangia 2021 experiment
Resubmit Astrangia review manuscript
Finish intro and methods for e5 ncRNA paper
Diversity statement for dissertation proposal

Sample processing

Finish miRNA library prep (8 samples)
Library prep for WGBS (27 samples)
Carbs for DT samples
Extractions, library prep, lipid extraction when AH is here

Data analysis

Finish stats for Astrangia 2021 phys data (carbs)
Work on Astrangia 2021 mRNA functional enrichment analysis
Run DESeq2 on miRNAs
Continue with genome assembly for Apul
Troubleshoot Pacuta goseq
Test miranda

Daily log

March 1

Section 1 miRNA library prep test with 2 samples
Worked on dissertation proposal hypotheses
Read methods of new Ofav PacBio genome paper !!!!!
Read Zoe methods proposal
GSA event
Raw read length analysis for Apul genome
Finished writing switchfree protocol
Made OSF repo for Apul genome

March 3

Rest of miRNA library prep test with 2 samples + QC
Worked on dissertation proposal + appendices
Ran euk contaminant read identifier

March 4

Looked at contaminant euk output
miRNA library prep with 2 samples + QC
Emailed Kevin Bryan re CPC2 and viral/prok genomes on Andromeda
Worked on dissertation proposal
Edited Astrangia review figure + manuscript
Restarted hifiasm
Worked on writing up pico protocol
Qubit on miRNA libraries
Writing up miRNA library prep posts

March 5

Prepped tubes for miRNA library prep tomorrow
Moved RiboFree libraries into tubes to send to sequencer
Wrote up rest of pico protocol
Cleaned and swapped out egg crate for BT 3/4
Lab meeting
Made miRNA gene count matrix!!!!!! and combined it with info about filtered novel and known miRNAs
DIBP workshop
Cleaning up miRNA R code
Prok and viral blast against Apul hifi reads

March 6

Looked at viral contam, still waiting for prok to finish
miRNA library prep section 1, 2, 3
Worked on e5 ncRNA intro
Gathering protein sequence info re ncRNA machinery
Lab meeting

March 7

miRNA library prep section 4 + QC
GOSeq for Pacuta HI 2022
Ordered dry ice
Started making sample submission sheet

March 8

Goseq and biomin analysis for Pacuta
Meeting with Caroline
e5 ncRNA meeting
Serena defense

March 9

Writing a little for Pacuta paper

March 11

Worked on intro/discussion + results for Pacuta paper
Restarted prok blast script
Interpreted hifiasm output (contam sequences not removed)
Ran Busco for hifiasm assembled contigs
Functional enrichment + biomin analysis + figure making for Pacuta paper - got lots done today
Looked at busco results - much better than canu, hifiasm is the way to go for assembly with this data
Blast for Pacuta and Spist subset biomin genes

March 12

Wrote/read a bit about collagen for Pacuta paper
Finished sample sheet for Genohub
Writing meeting
Finished edits for Astrangia review paper
Methods and results for Pacuta paper
Remaking figures for Pacuta paper
Made carb chem table for Pacuta paper
Made supplemental tables file for Pacuta paper

March 13

Restarted Pacuta biomin genes blast script
Posted reef bites article
Sent Astrangia review paper back to HP
Making new figures for Pacuta paper
Wrote results + discussion portions for Pacuta paper
Lab meeting
Restarted prok blast script

March 14

SELF CARE DAY!!!!!!!!
Restarted Pacuta blast script - failed
Wrote settlement and survivorship paragraphs for Pacuta discussion

March 15

Cleaned aquarium room

March 16

Prok and viral filtering for Apul genome
Made a list of filtered reads to use in genome assembly

March 18

Shipped samples to OK! Yay
Wrote up shipping and receiving protocol for putnam lab wiki
Helped Zoe with some aquarium room stuff
Met w/ Chloe
Read paper for jclub and took notes
Submitted TAR for Temperate Coral Conference

March 19

DESeq2 on miRNAs for Astrangia 2021
Reading paper for jclub
Lab meeting
Aquarium room stuff
Counseling center mtg
Trying to filter for mRNA and miRNAs of interest in Astrangia 2021 data, realizing I need to predict 3’ UTR regions in the genome data…
Starting blast script for miRNA against mRNAs in Astrangia 2021
Reran prok and viral filtering for Apul genome
Meeting w/ Federica

March 20

Ordered ln2
Filtering reads that passed contam filtering from hifi raw reads
Blastn w/ mRNAs + miRNAs as query keeps failing, blastx w/ prot seqs worked
Trying to QC cleaned reads (need to email Kevin Bryan to install)
Started initial hifiasm run
Lab meeting
Ordered glasses!
Filled out therapy forms
Hollie updates

March 21

Attempted to isolate 3’UTR sequences using bedtools, was unsuccessful
Talked w/ Zoe re quals and 3’UTR
Added delegates on ecampus for TARs
lncRNA discovery for AST 2021! woohoo!
Running kallisto for lncRNA quantification in my AST 2021 samples
Posted/scheduled reefbites articles

March 22

BLASTing lncRNAs against genome, prot, smRNA and mRNA for AST 2021
e5 ncRNA meeting

March 25

Looked at lncRNA blast AST 2021 results
busco and quast on hifiasm initial assembly + haplotypes
Started temperate coral conference abstract
Led DIBP workshop
Made beads for switchfree library prep
Did some 3’UTR extraction w/ Javi script
Talked w/ Ariana re lab work this week
Met w/ Zoe
3’UTR fasta creation!
Busco + quast QC interpretations
hifiasm iteration scripts running

March 26

Diluted DNA for ITS2
Talked w/ Ariana about plan for the week
Tried to run miranda, failed. need to reinstall conda miranda
Labeled tubes for extractions + PCR
miranda running successfully!
Therapy
Random aquarium stuff
Found random samples
ncRNA protein machinery NCBI search
Reviewed Astrangia manuscript for ICB journal

March 27

Wrote some methods in overleaf for Apul genome
Extractions + QC for 10 Poc larval samples
Discussions with Ariana and Hollie
Met w/ Zoe
Notebook posts

March 28

Tapestation for 6 RNA samples
PCR for ITS2 samples
Dropped off sanger samples
Looked at miranda output
Started new miranda run w/ different parameters
RNASeq samples back! Yay
Started running QC + trimming on DT RNASeq samples
ITS2 gel w/ Ariana
Random aquarium stuff

March 29

QC + alignment for DT Mcap 2023
Edits to Astrangia review manuscript
Trying to remake fig 4 for review manuscript
QC for s30 hifiasm assembly (busco + quast)
Looked at busco results for primary s30 assembly
Alignment + assembly for DT Mcap 2023 + gene count matrix
Sarah Donelan talk
3’mRNA library prep

March 31

QC for 3’mRNA library prep
Catching up on notebook posts

March reflection

How did I do with my goals for this month?

Writing and manuscripts

Full draft of dissertation proposal - nope
Write physiological results for Astrangia 2021 experiment - nope
Resubmit Astrangia review manuscript - nope, but got edits back from Hollie. Once I make the revisions, I will resubmit
Finish intro and methods for e5 ncRNA paper - still working on it
Diversity statement for dissertation proposal - working on it

Sample processing

Finish miRNA library prep (8 samples) - done!
Library prep for WGBS (27 samples) - nope
Carbs for DT samples - nope
Extractions, library prep, lipid extraction when AH is here - successfully extracted and prepped samples from POC 2023 spawning

Data analysis

Finish stats for Astrangia 2021 phys data (carbs) - nope
Work on Astrangia 2021 mRNA functional enrichment analysis - nope
Run DESeq2 on miRNAs - yes
Continue with genome assembly for Apul - did a lot of genome things this month, making good progress. Currently at the assembly portion
Troubleshoot Pacuta goseq - goseq complete! Did a lot of work on Pacuta paper this month. I did lots of methods/results/discussion writing, along with functional enrichment analysis.
Test miranda - successfully ran miranda test! Need to figure out which flags will invoke strict seed binding

I felt pretty productive this month, even if its not reflected in the goals I set for myself (though I should try to stay on task).

Written on March 1, 2024