Need public (human) RNA-seq data: paired-end, 4+ replicates per group

[turnersd]

The title pretty much says it all. I'm trying to put together a workshop and I need some public RNA-seq data.

More specifically, I need Illumina paired-end RNA-seq data from 2 conditions with at least four replicates per condition. Preferably in human. As I'm going to do some comparisons between cufflinks/cuffdiff and DEXSeq, ideally the data would result from an experiment messing around with some splicing factors so we have some interesting alternative splicing / exon use results to look at. I need four replicates in at least one group because I'm going to do the same experiment they did in the DEXSeq manuscript - comparing controls to controls to see how many "significant" results each method finds when ideally they shouldn't find any.

I've searched around GEO/SRA (limiting by platform - GAIIx or HiSeq) and I couldn't find anything that met my needs.

Any suggestions?

[dietmar13]

i have used this:

SRA043728 by BCCAGSC on 2011-10-27 17:30:00

12 vs. 12 matched pairs colon cancer vs normal mucosa.


the authors used this data set for characterisation of bacteria responsible for colon caner, but i have used it successfully for validation of differential expression-pipelines.

read depth are only about 2 mio per sample, therefore probably too low for alternative splicing analysis...

[turnersd]

Thanks dietmar13. I did take a look but 2M/sample is pretty low to robustly look at splicing. I will keep this one bookmarked though. Thanks again.

[davidblaney]

Any luck

Hi,

I'm looking for a similar kind of data set and just wondered if you had any luck?

Thanks

[turnersd]

Hi,

I'm looking for a similar kind of data set and just wondered if you had any luck?

Thanks

Nope. Lots of mouse data though.