Question: Publicly available Rna-Seq count data
0
gravatar for Naim.Mahi
4.2 years ago by
Naim.Mahi40
University of Cincinnati College of Medicine, Cincinnati, OH, USA
Naim.Mahi40 wrote:

Dear Altruists,

I am looking for some sources that provides publicly available rna-seq raw/processed count data for free download. Specifically, I am in need of some Illumina HiSeq produced data sets with roughly 100bp PE sequencing.

Please let me know if you have anything in mind.

TIA.

sequencing rna-seq next-gen • 2.2k views
ADD COMMENTlink modified 4.2 years ago by matted7.1k • written 4.2 years ago by Naim.Mahi40
1
gravatar for Daniel Swan
4.2 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

I'm sure the SRA would oblige: http://www.ncbi.nlm.nih.gov/sra/?term=RNA-Seq

ADD COMMENTlink written 4.2 years ago by Daniel Swan13k

Thank you :)

ADD REPLYlink written 4.2 years ago by Naim.Mahi40
1
gravatar for Manvendra Singh
4.2 years ago by
Manvendra Singh2.1k
Berlin, Germany
Manvendra Singh2.1k wrote:

I think TCGA data would be good to start with,

https://tcga-data.nci.nih.gov/tcga/tcgaDownload.jsp

 

It has all formats of data, I think level 3 is RNA-seq

kindly check it once

 

ADD COMMENTlink written 4.2 years ago by Manvendra Singh2.1k

Thank you :)

ADD REPLYlink written 4.2 years ago by Naim.Mahi40
1
gravatar for matted
4.2 years ago by
matted7.1k
Boston, United States
matted7.1k wrote:

Check out the ReCount database.  They state:

"ReCount is an online resource consisting of RNA-seq gene count datasets built using the raw data from 18 different studies. ... The count tables, ExpressionSets, and phenotype tables are ready to use and freely available here.  By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward."

ADD COMMENTlink written 4.2 years ago by matted7.1k

Thank you. I checked their website earlier, but their data sets are quite old. My supervisor is not quite satisfied with these data sets :\

ADD REPLYlink written 4.2 years ago by Naim.Mahi40
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