Posts
Samples Received - Pacific Oyster Tissues from Hawaii (Maria Haws) from High and Low pCO2
We received frozen Crassostrea gigas tissues from Maria Haws in Hawaii, as part of a pCO2 experiment. Tissues include:
Data Wrangling - Renaming, Splitting, and Feature Counts of Updated Pgenerosa_v074 GenSAS Merged GFF
In the final GFF from our GenSAS Pgenerosa_v074.a4 annotation , we noticed that there were no repeat motifs/sequences identified on Scaffold 01. The remaining scaffolds all had repeat motifs present on them, so something seemed amiss (see this GitHub Issue for more info).
PCR - Crassostrea gigas and sikamea Mantle gDNA from Marinelli Shellfish Company
I ran this PCR a couple of times before and, embarrassingly, I had ordered/used the wrong primers.
Samples Received - C.bairdi Hemolymph and Tissue in Ethanol from Pam Jensen
Pam Jensen (NOAA) brought by a variety of hemolymph and tissues stored in ethanol to use for DNA sequencing with the new MinION (Oxford Nanopore) to help aid our transcriptomics work.
qPCR - Geoduck hemolymph and hemocyte cDNA with vitellogenin primers
Previously isolated RNA on 20191125 and made cDNA on 20191126 from some geoduck hemolymph and hemocyte samples that Shelly asked me to run qPCRs on.
Reverse Transcription - P.generosa DNased Hemolypmh and Hemocyte RNA from 20191125
Performed reverse transcription on the DNased hemolymph and hemocyte RNA from yesterday.
RNA Isolation and Quantification - Geoduck hemolymph and hemocyte samples
Shelly asked me to isolate RNA and run some qPCRs on the following samples:
PCR - Crassostrea gigas and sikamea Mantle gDNA from Marinellie Shellfish Company - No Multiplex
UPDATE 20191125
PCR - Crassostrea gigas and sikamea Mantle gDNA from Marinelli Shellfish Company
UPDATE 20191125
Data Wrangling - Rename Pgenerosa_v074 Bismark Coverage Files Scaffold Names
After a meeting today, Steven and Hollie realized that the Bismark coverage files were still using the old scaffold names, stemming from the Pgenerosa_v074 naming. I’d previously updated filenames and scaffold names, so I recycled some of the code used there to rename the coverage files.