What Databases Are Available For Rna-Seq Datasets?
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9.1 years ago
aprathke ▴ 140

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).

rna-seq database geo • 45k views
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The following search does find quite a few RNA-seq data sets in GEO:

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

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9.1 years ago
Geparada ★ 1.4k

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!

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9.1 years ago
Konrad ▴ 690

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.)

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9.1 years ago
aprathke ▴ 140

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.

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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.

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9.1 years ago
Nianxiang ▴ 10

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

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