Dataset request: RNA-seq experiment that uses both single and paired end data with multiple experimental conditions

Question

[endrebak]

I want to find an RNA-seq experiment that uses both single and paired end data with multiple experimental conditions. It should be available in the public domain.

Do any of you know such a dataset? If not, how can I search online databases to find such a dataset?

Thanks,

Endre

Answer 1

[Carlo Yague]

Hi,

There is this paper on drosophila. Raw data is available on GEO.

"The samples were [...] sequenced on an Illumina Genome Analyzer II using either single-read or paired-end protocols (Illumina)."

Note that the data is already summarized at the gene/exon level in the pasilla package.

[endrebak]

Upvoted. Will accept when I get it downloaded :) Thanks :) Other suggestions also welcome :)

[endrebak]

Do you understand why they say "GSM461176–GSM461181" when GSM461182 etc are also seemingly from the same experiment? E.g. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM461182

[Carlo Yague]

From what I understand, the data belong to the modENCODE consortium that lead to several publications, including this one. So the full serie (GSE18508) includes data from the full consortium, but only GSM461176 to GSM461181 is relevant to the publication.