30 April 2024
Tuesday
29 April 2024
Monday
26 April 2024
Friday
25 April 2024
Thursday
trying to make some figures for cod DEGs
class (fsh541) – Laura wasour instructor today!
lab meeting
tissue subsampling (cod liver tissue, compiling methylation samples)
24 April 2024
Wednesday
class, GNM569 (last class!)
continuing cod HISAT run
applied for some QSCI TA positions in the fall quarter
23 April 2024
Tuesday
22 April 2024
Monday
class – GNM569
E5 analyses … still…
finished GNM569 project2
classwork for FSH541 tomorrow
19 April 2024
Friday
E5 meeting
continued rerunning analyses – realized I didn’t use the curated miRBase+cnidarians database from Jill, so I actually need to re-rerun pretty much everything 😭
classwork for GNM569
18 April 2024
Thursday
pubathon
class (FSH541)
lab meeting, talked about figures
continued rerunning E5 sRNA analyses
17 April 2024
Wednesday
class (GNM569)
finished mirdeep2 run with merged reads for E5. Tried to get started on the P.meandrina rerun, but I can’t access the reads online? Something’s up with Owl and I can’t access things stored there 😳
got references for everything I cited to far in cod manuscript and inserted the in-text citations
updated the readme file for the cod repo
more working on GO enrichment analysis for the cod rnaseq data. I figured out the annotation/making an ID-GO database step, now I’m trying to do the actual enrichment (nothing about this on the lab website, so trying to look through Matt’s code)
reading and quiz for FSH541
16 April 2024
Tuesday
classwork (FSH541)
updating cod methylation sample list again, per my discussion with Laura yesterday
class (FSH541)
lab class (FSH541) – working on getting a HiSat workflow for aligning cod rnaseq reads to genome (note I already have a transcriptome pseduoaliignment and count matrix using kallisto, this is just an exercise)
mariners game tonight with the cohort!
15 April 2024
Monday
class (GNM569)
rerunning BLAST and miRdeep2 with merged P.eve reads. Having some trouble with miRdeep2, I think the merging introduced reads <17bp long, which miRdeep2 doesn’t like.
meeting with laura about cod project. discussed adjusting samples selected for methylation to ensure full representation of genetic diversity.
12 April 2024
Friday
Out
11 April 2024
Thursday
class (FSH 541)
classwork
starting on rerunning E5 sRNAseq analyses using merged reads. starting with P.eve.
10 April 2024
Wednesday
GNM569 class
last edits for GNM569 project, I’m just pushing what I have and walking the heck away🥴
classwork for FSH541
methods writing for cod manuscript
09 April 2024
Tuesday
classwork for FSH541
FSH541 Lecture
FSH541 Lab
more working on GNM569 project – at this point I actually never want to look at a terminal window again, so…. this class may be having the wrong effect on me lol
08 April 2024
Monday
- Literally just grinding the GNM569 project all day, at this point I’m seeing lines of bash script in my sleep
05 April 2024
Friday
E5 molecular meeting, committed to continuing the sRNA analyses with new merged reads
Grinding the GNM569 project for 6 hours straight and making almost no progress because the TA is being singularly unhelpful 😭
04 April 2024
Thursday
pubathon
meeting w/ Steven about oyster experimental setup (see notes here)
class (FISH541)
updating lab notebook for start of April (new posts/goals docs)
03 April 2024
Wednesday
class (GNM569)
classwork for GNM569
classwork for FSH541 – readings and quiz
meeting with Laura about cod DGE analysis — notes here
making some final edits to cod methylation sample list
lab trivia night :)
02 April 2024
Tuesday
FSH541 lecture
FSH541 lab
some writing on cod manuscript
01 April 2024
Monday
class (GNM569)
adding experimental metadata to cod DGE analysis and generating some PCAs with size included
classwork for FSH541 (reading, quiz)