Category Archives: SRA Submissions

Data Management – SRA Submission of Ostrea lurida GBS FASTQ Files

Prepared a short read archive (SRA) submission for archiving our Olympia oyster genotype-by-sequencing (GBS) data in NCBI. This is in preparation for submission of the mansucript we’re putting together.

I followed my outline/guideline for navigating the SRA submission process, as it’s a bit of a pain in the neck. Glad my notes were actually useful!

The following two files are currently being uploaded via FTP; the process will take about 3hrs, as each file is ~18GB in size:

 

They are being submitted under the following accession numbers (note: a final accession number will be provided once this is publicly available; I will update this post when that happens):

SRA Release – Transcriptomic Profiles of Adult Female & Male Gonads in Panopea generosa (Pacific geoduck)

The RNAseq data that I previously submitted to NCBI short read archive (SRA) has been released to the public today. Here are the various links for the project:

Study: SRP072283 – http://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP072283

 

BioProject: PRJNA316216 – http://www.ncbi.nlm.nih.gov/bioproject/PRJNA316216

Study: SRP072283 – http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP072283

Female Pool Experiment: SRX1659865 – http://www.ncbi.nlm.nih.gov/sra/SRX1659865

Male Pool Experiment: SRX1659865 – http://www.ncbi.nlm.nih.gov/sra/SRX1659866

SRA Submission – Genome sequencing of the Olympia oyster (Ostrea lurida)

Adding our Olympia oyster genome sequencing (sequencing done by BGI) to the NCBI Sequence Read Archive (SRS). The current status can be seen in the screen cap below. 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:

151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.gz
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.gz
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz

Paired-end sequencing files were uploaded together within a single “Run”.

SRA Info:
SRA: SRS1365663
Study: SRP072461
BioProject: PRJNA316624
BioSample: SAMN04588827

SRA Submission – Genome sequencing of the Pacific geoduck (Panopea generosa)

Adding our geoduck genome sequencing (sequencing done by BGI) to the NCBI Sequence Read Archive (SRS). The current status can be seen in the screen cap below. 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:

151114_I191_FCH3Y35BCXX_L1_wHAIPI023989-79_1.fq.gz
151114_I191_FCH3Y35BCXX_L1_wHAIPI023989-79_2.fq.gz
151122_I136_FCH3L2FBBXX_L7_wHAXPI023990-97_1.fq.gz
151122_I136_FCH3L2FBBXX_L7_wHAXPI023990-97_2.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHPANwalDDAADWAAPEI-101_1.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHPANwalDDAADWAAPEI-101_2.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHPANwalDDAADWAAPEI-101_1.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHPANwalDDAADWAAPEI-101_2.fq.gz
160103_I137_FCH3V5YBBXX_L5_WHPANwalDDABDLAAPEI-100_1.fq.gz
160103_I137_FCH3V5YBBXX_L5_WHPANwalDDABDLAAPEI-100_2.fq.gz
160103_I137_FCH3V5YBBXX_L5_WHPANwalDDACDTAAPEI-102_1.fq.gz
160103_I137_FCH3V5YBBXX_L5_WHPANwalDDACDTAAPEI-102_2.fq.gz
160103_I137_FCH3V5YBBXX_L6_WHPANwalDDABDLAAPEI-100_1.fq.gz
160103_I137_FCH3V5YBBXX_L6_WHPANwalDDABDLAAPEI-100_2.fq.gz
151114_I191_FCH3Y35BCXX_L2_wHAMPI023988-81_1.fq.gz
151114_I191_FCH3Y35BCXX_L2_wHAMPI023988-81_2.fq.gz
160103_I137_FCH3V5YBBXX_L6_WHPANwalDDACDTAAPEI-102_1.fq.gz
160103_I137_FCH3V5YBBXX_L6_WHPANwalDDACDTAAPEI-102_2.fq.gz

Mate pair sequencing files were uploaded together within a single “Run”.

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