Question: Looking for a cancer dataset for RNA-Seq workshop
3
gravatar for Nicolas Rosewick
2.8 years ago by
Belgium, Brussels
Nicolas Rosewick7.9k wrote:

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

workshop rna-seq data • 998 views
ADD COMMENTlink modified 2.8 years ago by i.sudbery5.0k • written 2.8 years ago by Nicolas Rosewick7.9k
2
gravatar for Amitm
2.8 years ago by
Amitm1.6k
UK
Amitm1.6k wrote:

One way is to go to ArrayExpress and search like this - Avlbl RNA-seq datasets

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. data sets 2

ADD COMMENTlink written 2.8 years ago by Amitm1.6k
0
gravatar for vakul.mohanty
2.8 years ago by
vakul.mohanty240
United States
vakul.mohanty240 wrote:

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.

ADD COMMENTlink written 2.8 years ago by vakul.mohanty240

The data from CCLE is freely available for download now

ADD REPLYlink written 2.8 years ago by vakul.mohanty240
0
gravatar for i.sudbery
2.8 years ago by
i.sudbery5.0k
Sheffield, UK
i.sudbery5.0k wrote:

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 The analysis methods might be a bit out of date now, but it would be interesting to compare what difference using up to date methods makes.

ADD COMMENTlink written 2.8 years ago by i.sudbery5.0k

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

ADD REPLYlink written 2.8 years ago by H.Hasani760

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.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by i.sudbery5.0k
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