Question: What Databases Are Available For Rna-Seq Datasets?
12
gravatar for aprathke
7.0 years ago by
aprathke140
aprathke140 wrote:

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).

geo database rna-seq • 38k views
ADD COMMENTlink modified 7.0 years ago by Khader Shameer18k • written 7.0 years ago by aprathke140

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

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

ADD REPLYlink written 7.0 years ago by Malachi Griffith17k
6
gravatar for Geparada
7.0 years ago by
Geparada1.4k
Cambridge
Geparada1.4k wrote:

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!

ADD COMMENTlink modified 7.0 years ago • written 7.0 years ago by Geparada1.4k
2
gravatar for Konrad
7.0 years ago by
Konrad690
Germany
Konrad690 wrote:

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.)

ADD COMMENTlink written 7.0 years ago by Konrad690
2
gravatar for aprathke
7.0 years ago by
aprathke140
aprathke140 wrote:

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.

ADD COMMENTlink written 7.0 years ago by aprathke140

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.

ADD REPLYlink written 7.0 years ago by Geparada1.4k
1
gravatar for Nianxiang
7.0 years ago by
Nianxiang10
Nianxiang10 wrote:

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

ADD COMMENTlink written 7.0 years ago by Nianxiang10
1
gravatar for Khader Shameer
7.0 years ago by
Manhattan, NY
Khader Shameer18k wrote:
ADD COMMENTlink modified 7.0 years ago • written 7.0 years ago by Khader Shameer18k
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