Normal Rna-Seq Data
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11.9 years ago
AsoInfo ▴ 300

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 • 4.6k views
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what is a "normal" RNA-SEQ data ?

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

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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.

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

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11.9 years ago

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

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Really Helpful.... Thanks!

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11.9 years ago
matted 7.8k

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.

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10.7 years ago
earonesty ▴ 250

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/

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11.9 years ago
Vikas Bansal ★ 2.4k

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.

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11.9 years ago

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.

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