Posts
DNA Isolation and Quantification - C.bairdi Hemolymph Pellets in RNAlater
Isolated DNA from the following 23 samples:
RNA Isolation and Quantification - C.bairdi Hemolymph Pellets in RNAlater
TL;DR - Recovered absolutely no RNA from any sample! However, I did recover DNA from each sample.
Lab Maintenance - Cluster UPS Battery Replacement
Replaced the batteries on one of the APC uninterruptable power supplies (UPS) on our local server cabinet.
DNA Quality Assessment - Agarose Gel and NanoDrop on C.bairdi gDNA
I isolated C.bairdi gDNA yesterday (20200108) and now want to get an idea if it’s any good (i.e. no contaminants, high molecule weight).
DNA Isolation and Quantification - C.bairdi gDNA from EtOH Preserved Tissue
I isolated gDNA from ethanol-preserved C.bairdi muscle tissue from sample 20102558-2729 (SPNO-ReferenceNO). This sample was chosen as it had 0 in the SMEAR_result and BCS_PCR_results columns, indicating it should be free of Hematodinium. See the sample spreadsheet linked below for more info.
Reagent Prep - RNA Pico Ladder Aliquoting and Testing
Created aliquots of RNA Pico Ladder received on 20191101, per the manufacturer’s instructions. Created single-use aliquots of 1.5uL and stored at -80oC:
Transcriptome Annotation - C.bairdi Trinity Assembly Trinotate on Mox
After performing de novo assembly on our Tanner crab RNAseq data on 20191218 and performing BLASTx annotation on 20191224, I continued the annotation process by running Trinotate.
Transcriptome Annotation - C.bairdi Trinity Assembly BLASTx on Mox
In preparation for complete transcriptome annotation of the C.bairdi de novo assembly fro 20191218, I needed to run BLASTx. The assembly was BLASTed against the SwissProt database that comes with Trinotate. Initial BLAST output format selected was format 11 (i.e. ASN format), as this allows for simple conversion between different formats later on, if desired.
Transdecoder - C.bairdi De Novo Transcriptome from 20191218 on Mox
Ran Trinity to de novo assemble the C.bairdi RNAseq data we had on 20191218 and now will begin annotating the transcriptome using TransDecoder on Mox.
Transcriptome Assembly - C.bairdi Trimmed RNAseq Using Trinity on Mox
Earlier today, I trimmed our existing C.bairdi RNAseq data, as part of producing generating a transcriptome (per this GitHub issue). After trimming, I performed a de novo assembly using Trinity (v2.9.0) with the stranded library option (--SS_lib_type RF) on Mox.