Posts
MBD Enrichment - DNA Quantification of C.virginica MBD Samples from 20190312
Finished MBD enrichment on 20190312 using the MethylMiner kit. Since we were out of Qubit assay tubes, I could not quantify these samples when I initially completed the ethanol precipitation. Tubes are in, so I went forward with quantification using the Roberts’ Lab Qubit 3.0 and the 1x High Sensitivity dsDNA assay.
Transcriptome Annotation - Geoduck Gonad with BLASTx on Mox
I’ll be annotating the transcriptome assembly (from 20190215) using Trinotate and part of that process is having BLASTx output for the Trinity assembly, so have run BLASTx on Mox.
Transcriptome Annotation - Geoduck Ctenidia with BLASTx on Mox
I’ll be annotating the transcriptome assembly (from 20190215) using Trinotate and part of that process is having BLASTx output for the Trinity assembly, so have run BLASTx on Mox.
Data Management - Create C.virginica Bisulfite Genome with Bismark on Mox
In preparation for some a bisulfite analysis requested by Steven, I needed to make bisulfite genome with, and for, Bismark to use and wanted to use the same one Yaamini has been working with. Downloaded the NCBI version of the C.virginica genome.
MBD Enrichment - Ethanol Precipitation of C.virginica MBD samples
After completing two rounds of MBD enrichment (first 12 samples on 20190307 and the second 12 samples on 20190311), I performed ethanol precipitation, per the MethylMiner instructions with the following modifications:
MBD Enrichment - C.virginica Sheared Mantle DNA from 20190306
Last week I performed MBD enrichment on 12 of the 24 Lotterhos C.viriginica mantle DNA on samples I had sheared on 20190306. I proceeded with MBD enrichment using the MethylMiner Kit (Invitrogen) on the 12 remaining samples of the 24. I followed the manufacturer’s protocol for input DNA >1ug - 10ug with the following modifications:
MBD Enrichment - C.virginica Sheared Mantle DNA from 20190306
Yesterday, I sheared the Lotterhos C.virginica gDNA in preparation for MBD enrichment. Today, I proceeded with MBD enrichment using the MethylMiner Kit (Invitrogen) on 12 of the 24 samples. I followed the manufacturer’s protocol for input DNA >1ug - 10ug with the following modifications:
DNA Shearing & Bioanalyzer - Lotterhos C.virginica Mantle gDNA from 2018114
Crassostrea virginica mantle gDNA that had previously been isolated on 20181114 was evaluated for integrity via agaroase gel yesterday (20190305). Everything looked pretty good, so proceeded with shearing in preparation for MBD enrichment.
Agarose Gel - Lotterhos C.virginica Mantle DNA from 20181114
Checked DNA integrity of the Crassostrea virginica mantle gDNA I isolated on 20181114 in preparation for MBD enrichment. Detailed sample info and sample processing (including calculations for MBD enrichment using the MethylMiner Kit) are here (Google Sheet):
Data Management - Data Migration and Drive Expansion on Gannet
A little while ago, we installed some additional hard drives in Gannet (Synology RS3618XS) with the intention of expanding the total storage space. However, the original set of HDDs were set up as RAID10. As it turns out, RAID10 configurations cannot be expanded! So, the new set of HDDs were configured as a separate volume (Volume 2) in a RAID6 configuration. After backing up the /volume1/web directory (via rsync) to our UW Google Drive, I begane the data migration.