Looking for a cancer dataset for RNA-Seq workshop

Question

[Nicolas Rosewick]

Hi,

For a RNA-Seq practical course I organize soon for my university I'm looking for a publication with publicly available data set (raw fastq would be great) on a cancer study (transcriptome analysis). The idea will be to redo the paper analysis from the raw data (alignment, expression analysis, etc...) .

Any idea ?

Thanks

Answer 1

[Amitm]

One way is to go to ArrayExpress and search like this -

Not all studies might be relevant though, but a good resource nonetheless. The 'green wave' symbol links to ENA wherefrom you can download fastq. You could search directly on ENA but the user interface here is clunky.

Another resource is NCBI GEO. Here again apply filters to arrive to possibly useful datasets.

Answer 2

[vakul.mohanty]

GDC (https://gdc-portal.nci.nih.gov/) should have data from Cancer Cell Line Encyclopedia (CCLE) sometime this month if you can wait a little.

[vakul.mohanty]

The data from CCLE is freely available for download now

Answer 3

[i.sudbery]

We've put a dataset out there that I have used before in workshops:

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48403

Its 7 prostate cancer samples, pre and post treatment. The analysis methods might be a bit out of date now, but it would be interesting to compare what difference using up to date methods makes.

[H.Hasani]

I wonder if you have tried to call variants from your data?

[i.sudbery]

I have, but was early, before there was GATK best practice for RNA-seq I believe. The results were i bit of a mess and ii ad a hard time pulling any signal from the noise. It could almost certainly be done better now.