Source for Normals for Bladder Cancer RNA-Seq

Question

[Ron]

Hi ,

I am looking for Normal Samples for Bladder as well as Prostate to compare with their respective cancer counterparts.

Can anyone provide good sources of data?

Thanks,
Ron

[Phil S.]

You maybe find some useful sequences in the SRA

Answer 1

[Amitm]

Hi,

Notwithstanding the rider regarding combining RNA-seq studies, the GTEx portal is meant to be a repository of normal tissue expression profiling. I checked and you have bladder (11 samples) and prostate samples (106 samp.) available.

The data is freely (academic usage) available and in two formats: count and FPKM variants.

If you apply proper normalization strategies, these datasets might be of use to you.

Another rider, the RNA source is autopsy tissue.

Answer 2

[igor]

You should be very careful about combining RNA-seq from multiple sources. Most of the differences you find will be due to differences in sample and library preparation.

In general, probably the best resource for expression data sets is GEO: http://www.ncbi.nlm.nih.gov/gds/