Question: Normal Rna-Seq Data
1
gravatar for AsoInfo
7.5 years ago by
AsoInfo280
Bonn, Germany
AsoInfo280 wrote:

Hello there,

I have a small question, Is it possible to have a normal RNA-SEQ data available because I searched in GEO datasets and ENCODE but I didn't succeed.

If yes, then please let me know about the link or web address.

Thanks in advance!

EDIT

Thank you so much for your replies!

The species is Homo sapiens.

The term "normal" means not abnormal or related to any disease. Because I have some cancer rna data and I want to include one "Normal Control" rna data for comparison.

I hope, I cleared the queries.

Thanks!

rna-seq • 3.2k views
ADD COMMENTlink modified 6.3 years ago by earonesty230 • written 7.5 years ago by AsoInfo280
2

what is a "normal" RNA-SEQ data ?

ADD REPLYlink written 7.5 years ago by Arun2.3k

Yes, please clarify. Do you mean "normalized"? Or perhaps, not "abnormal"?

ADD REPLYlink written 7.5 years ago by Neilfws48k

I've edited your question to add the information you had provided as an answer. Please note you can 'edit' your question to modify it or add details.

ADD REPLYlink written 7.5 years ago by Leonor Palmeira3.7k

Thanks, leonor... Your advice is noted....

ADD REPLYlink written 7.5 years ago by AsoInfo280
3
gravatar for Leonor Palmeira
7.5 years ago by
Leonor Palmeira3.7k
Liège, Belgium
Leonor Palmeira3.7k wrote:

Have you looked in SRA?

The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD® System, Helicos Heliscope®, Complete Genomics®, and Pacific Biosciences SMRT®.

For instance:

http://www.ncbi.nlm.nih.gov/sra?term=rna-seq

ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by Leonor Palmeira3.7k

Really Helpful.... Thanks!

ADD REPLYlink written 7.5 years ago by AsoInfo280
1
gravatar for matted
7.5 years ago by
matted7.2k
Boston, United States
matted7.2k wrote:

You might look at the resource "ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets," available here:

http://bowtie-bio.sourceforge.net/recount/

They have mapped datasets and count tables for a set of relatively "high-profile" RNA-seq experiments, as well as links back to the raw data for each experiment. Several human tissue types are listed, which may help you match to your experiment more closely. However, in general, I would be wary of drawing conclusions from comparisons of very unmatched experiments.

ADD COMMENTlink written 7.5 years ago by matted7.2k
1
gravatar for earonesty
6.3 years ago by
earonesty230
United States
earonesty230 wrote:

GTEX is a big NIH study with "normal" (aka: healthy fresh-frozen tissue) RNA seq data. You can download the bams, convert to fastq - then put through the same pipe you put your diseased tissue though, then get the differences. It works very well. You'll need to apply for the data, it's controlled.

http://www.broadinstitute.org/gtex/

ADD COMMENTlink written 6.3 years ago by earonesty230
0
gravatar for Vikas Bansal
7.5 years ago by
Vikas Bansal2.4k
Berlin, Germany
Vikas Bansal2.4k wrote:

As you did not mention any species, which RNA-seq etc, I just searched randomly in GEO dataset. Here is the link

If you want to search in GEO for something specific, you can use Advance option from here.

ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by Vikas Bansal2.4k
0
gravatar for Sean Davis
7.5 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

While not directly addressing your question, you might take a look at using the GEOmetadb and SRAdb Bioconductor packages to do searches of GEO and SRA.

ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by Sean Davis25k
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