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
•
written
by
endrebak
1 answer
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.
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
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.
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