Question: Obtaining RNA seq data from NCBI
0
gravatar for saadleeshehreen
5 months ago by
saadleeshehreen60 wrote:

Hi,

I am looking for RNA seq data of some pseudomonas aeruginosa (100 genomes). I have assembly number (e.g. Assembly: GCF_000750905.1) for those genomes. I am not sure all of them have publicly available RNA seq data or not. How can I obtain corresponding RNA seq data ( SRA files) for those genomes?

Cheers

rna-seq • 244 views
ADD COMMENTlink modified 5 months ago by shivangi.agarwal80050 • written 5 months ago by saadleeshehreen60

For SRA files, you can refer GEO (Gene Expression Omnibus) database.

ADD REPLYlink written 5 months ago by shivangi.agarwal80050

I understand that. But I can't figure out how to retrieve SRA id of corresponding GCF id? For example, I couldn't manage to find any SRA file for GCF_000750905.1.

ADD REPLYlink written 5 months ago by saadleeshehreen60
0
gravatar for genomax
5 months ago by
genomax64k
United States
genomax64k wrote:

You can find the corresponding genome entry at EBI-ENA here. It appears that the submitter's only submitted finished genome sequence (and not the raw data). According to the linked paper the genome was sequenced on Roche 454.

ADD COMMENTlink modified 5 months ago • written 5 months ago by genomax64k
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