Question: Dataset request: RNA-seq experiment that uses both single and paired end data with multiple experimental conditions
0
gravatar for endrebak
2.1 years ago by
endrebak810
github.com/endrebak
endrebak810 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 • 745 views
ADD COMMENTlink modified 2.1 years ago by Carlo Yague4.9k • written 2.1 years ago by endrebak810
3
gravatar for Carlo Yague
2.1 years ago by
Carlo Yague4.9k
Canada
Carlo Yague4.9k 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 2.1 years ago by Carlo Yague4.9k

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

ADD REPLYlink written 2.1 years ago by endrebak810

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 2.1 years ago by endrebak810
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 2.1 years ago by Carlo Yague4.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1577 users visited in the last hour