Tag Archives: 4M

SRA Submission – Individual Transcriptomic Profiles of C.gigas Before & After Heat Shock

RNA-seq experiment conducted by Claire in 2013.

She sampled mantle tissue from three adult oysters, allowed them to recover from the sampling (one week?) and then subjected those same oysters to a 1hr heat shock at 40C and collected mantle tissue from them again.

As this is our first Small Read Archive (SRA) submission in many years, I decided to submit these to the SRA due to the small number of samples (6) from the Illumina sequencing we had done to make sure it was manageable.

An overview of the basic SRA submission process is here.

The current status can be seen in the screen cap below. Current release date is set for a year from now, but will likely bump it up. Need Steven to review the details of the submission (BioProject, Experiment descriptions, etc.) before I initiate the public release. Will update this post with the SRA number once we receive it.

Here’s the list of files uploaded to the SRA:

2M-HS_CCGTCC_L001_R1_001.fastq.gz
2M_AGTCAA_L001_R1_001.fastq.gz
4M-HS_GTCCGC_L001_R1_001.fastq.gz
4M_AGTTCC_L001_R1_001.fastq.gz
6M-HS_GTGAAA_L001_R1_001.fastq.gz
6M_ATGTCA_L001_R1_001.fastq.gz

SRA Accession: SRP072251

RNA Seq – C.gigas Total RNA from Claire’s Pre/Post Heat Shock

Shipped (dry ice) ~15ug of total RNA from each of the following samples to Genewiz, Inc for high throughput transcriptomic sequencing (Illumina HiSeq2500, 100bp, single end).

  • 2M – 33uL
  • 4M – 41uL
  • 6M – 15.6uL
  • 2M HS – 15uL
  • 4M HS – 12.2uL
  • 6M HS – 15.2uL

Here’s Claire’s notebook entry on their isolation and quantification:

http://claireeolson.blogspot.com/2014/10/rna-extractions.html