What Databases Are Available For Rna-Seq Datasets?

Question

[aprathke]

Currently, I'm looking into the Gene Expression Omnibus. Are there any other good websites that curate RNA-seq data (or perhaps provide links to where RNA-seq data can be found)? A bit of background: I'm looking for any publicly available RNA-seq data sets containing at least 10 individuals with some form of cancer (ideally breast cancer).

[Malachi Griffith]

The following search does find quite a few RNA-seq data sets in GEO:

http://www.ncbi.nlm.nih.gov/gds?term=rna-seq

Answer 1

[Geparada]

At ENCODE dashboard are available tones of RNA-seq experiments made from different cell lines. I'm analysing a lymphoblastoid cell line (GM12878), but I bet you will find a cell line derived from breast cancer or other type.

Cheers!

Answer 2

[Konrad]

Such RNA-Seq data sets can also be found at the Sequence Read Archive (SRA). (I am not sure if the old sets are moved to GEO after the funding of SRA was cut but I don't think so.)

Answer 3

[aprathke]

Thank you for the suggestions. So far, have been using TCGA and downloaded this BRCA data set. Wish there was some way to tell how many individuals this data set contains and if each unique identifier represents an individual.

Also, another good ENCODE list of RNA-seq data can be found here.

[Geparada]

Well I forgot mention TCGA! The dashboard should have the same information that in the list of ENCODE that you found, but at the dashboard the information are nicely organized.

Answer 4

[Nianxiang]

You can take a look at dbGAP and CGhub as well.

Answer 5

[Khader Shameer]

• RNAseq data of 60 CEU individual at 1000genomes
• RNAseq data at ENA