20240131
Coral E5 (GitHub repo)
- Messed around with BBtools for merging and/or trimming paired sRNA-seq reads. Seems like this won’t work, on either front!
20240130
Miscellaneous Lab Stuff
Helped Chris troubleshoot her SOD assay standard curve. She felt like her samples SOD activity was too low and falling outside of the standard curve.
Tried to evaluate BCA results - no raw data, though.
Looked through the SOD protocol.
Confirmed that her samples fell within the standard curve of the SOD assay and that everything was A-OK!
Went to eye doctor, eyes dilated, and couldn’t see/read anything for the rest of the day!
Coral E5 (GitHub repo)
- Continued to explore sRNA-seq read trimming options.
20240129
CEABIGR (GitHub repo)
- Did more work on exon stuff.
Coral E5 (GitHub repo)
- Read through a few papers about sRNA-seq trimming/analyses.
20240126
Science Hour
- Worked on more CEABIGR (GitHub repo) exon stuff with Steven.
20240125
Lab Meeting
- Read Ch.5 of “Race After Technology”
CEABIGR (GitHub repo)
Weekly meeting.
Explored exon coverage with Steven.
20240124
CEABIGR (GitHub repo)
- Implemented exon sum threshold to update ln(fold change vs Exon 1) determinations (Notebook).
20240123
Miscellaneous lab stuff
- Helped answer some questions Eric had regarding RNA isolation.
CEABIGR (GitHub repo)
- Worked extensively on exon sum threshold.
Coral E5 (GitHub repo)
- Answered some questions Danielle Becker had regarding Zymo’s RiboFree rRNA depletion and whether or not it works for marine organisms (does not work for marine molluscs…).
20240122
CEABIGR (GitHub repo)
Steven decided on exon coverage threshold of 100 reads (GitHub Issue).
Fleshed out more of the exon coverage threshold code.
Miscellaneous lab stuff
- Got updated quote for Cod WGBS (GitHub Issue).
20240119
Science Hour
Helped walk Eric (virtually) through lab to get ready for RNA isolations.
CEABIGR (GitHub repo)
- Continued work I started on setting exon coverage threshold.
20240111
- Started getting students Raven access for Steven’s course in Chile.
Coral E5 (GitHub repo)
Need to test out Azenta recommended trimming parameters.
Worked briefly on manuscript.
2024010
Lab meeting
CEABIGR (GitHub repo)
Yaamini and I reviewed spurious transcription data and determined some next steps:
Spurious transcription calcs associated with different levels of gene methylation.
Determine the slope of the ln(fold-change exon expression) per gene.
20240109
- Power outage all day…
20240108
In lab:
Sent replacement liver samples for Cod RNA-seq project (GitHub Issue).
Helped Noah get mercuric chloride waste transferred to EH&S carboys in FTR 228.
Had to do a fresh install of R on
swoose. Took awhile…
20240105
- Science Hour
CEABIGR (GitHub repo)
- Started to look into where (if?) we have methylation data on a per gene basis to plot vs. exon fold-change data from 20240103
20240104
Disabled Sensaphone input #3 due to frequent calls. This is the sensor for the “middle” -80oC freezer. This is an older freezer from a former professor, so I’m not sure we have any info on how to set it up, but I will see if I can figure out how to change the freezer temp limits, instead of disabling the Sensaphone.
Investigated a budget spending discrepancy issue (GitHub Issue).
Added a page about RStudio Server access on Raven on the tusk website, per this GitHub Issue.
20240103
CEABIGR (GitHub repo)
Worked extensively on calculating mean, natural log fold change of Exons 2 - 6, relative to Exon 1 expression across all genes, in all samples.
Generated line plots of the various possible comparisons.