Question: Dataset request: RNA-seq experiment that uses both single and paired end data with multiple experimental conditions
0
gravatar for endrebak
15 months ago by
endrebak760
endrebak760 wrote:

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

sequencing rna-seq • 514 views
ADD COMMENTlink modified 15 months ago by Carlo Yague4.4k • written 15 months ago by endrebak760
3
gravatar for Carlo Yague
15 months ago by
Carlo Yague4.4k
Belgium
Carlo Yague4.4k wrote:

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.

ADD COMMENTlink written 15 months ago by Carlo Yague4.4k

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

ADD REPLYlink written 15 months ago by endrebak760

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

ADD REPLYlink written 15 months ago by endrebak760
1

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.

ADD REPLYlink written 15 months ago by Carlo Yague4.4k
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