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Old 03-21-2012, 08:50 AM   #1
rskr
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Default Freely/Publically available transcriptome datasets

Are there any good places to find publicly and freely available transcriptome datasets including the raw reads preferably Illumina, for the purposes of publishing a resource paper?
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Old 03-21-2012, 09:41 AM   #2
Richard Finney
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Check out : http://www.ncbi.nlm.nih.gov/geo/quer...i?acc=GSE29158
You can download the raw reads.

This is this study : Toung JM, Morley M, Li M, Cheung VG. RNA-sequence analysis of human B-cells. Genome Res 2011 Jun;21(6):991-8. PMID: 21536721

It's the RNA seq of several "Coriell CEPH B-Cell" cell lines; so it's theoretically close to "normal rna-seq".

I used a model based alignment of this data to the genome (genome+refome+altspliceome+estome) approach.
These results are viewable at Cancer Genome Workbench under hg19 , "Cancer Genome Workbench - Miscellaneous Tracks" , UPENN_BCELL_NG_RNA

Just click on this URL ...
https://cgwb.nci.nih.gov/cgi-bin/hgT...LL_NG_RNA=full

You can zoom in and right click on the tracks to use Bambino to view the details.

This is one of the few good PUBLIC human rnaseq datasets. A lot of data is secret under US privacy laws.

Last edited by Richard Finney; 03-21-2012 at 09:44 AM.
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Old 03-21-2012, 09:51 AM   #3
rskr
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Quote:
Originally Posted by Richard Finney View Post
Check out : http://www.ncbi.nlm.nih.gov/geo/quer...i?acc=GSE29158
You can download the raw reads.

This is this study : Toung JM, Morley M, Li M, Cheung VG. RNA-sequence analysis of human B-cells. Genome Res 2011 Jun;21(6):991-8. PMID: 21536721

It's the RNA seq of several "Coriell CEPH B-Cell" cell lines; so it's theoretically close to "normal rna-seq".

I used a model based alignment of this data to the genome (genome+refome+altspliceome+estome) approach.
These results are viewable at Cancer Genome Workbench under hg19 , "Cancer Genome Workbench - Miscellaneous Tracks" , UPENN_BCELL_NG_RNA

Just click on this URL ...
https://cgwb.nci.nih.gov/cgi-bin/hgT...LL_NG_RNA=full

You can zoom in and right click on the tracks to use Bambino to view the details.

This is one of the few good PUBLIC human rnaseq datasets. A lot of data is secret under US privacy laws.
Thanks! that is pretty close to what I am looking for.
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Old 07-30-2012, 11:43 PM   #4
qqtwee
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Hi, are there any good places to find freely RNA-seq data of all or many different human cell lines ,and RNA-seq data of all or many different human tissue? If NCBI database can find this, how can I to find all these data?
I am looking forward to your reply. Best wishes! Thank you!
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Old 07-31-2012, 12:14 AM   #5
Simon Anders
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A good staring pint might be the ReCount resource: http://bowtie-bio.sourceforge.net/recount/

For different cell lines, look at the Encode project, and for different tissue types, maybe at the paper by Brawand et al. (Nature, 2011).
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Old 08-15-2012, 12:14 PM   #6
davisc
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ENCODE Link: http://genome-preview.ucsc.edu/cgi-b...CshlLongRnaSeq

Cheers.
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Old 08-21-2012, 12:49 AM   #7
Geoffreyion
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Well you can try out the link given below. May be it can work. It contains important information on transcriptome data sets. I get to know so much in detail about these data sets and believe me it's really good to know so much about it.
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Last edited by Geoffreyion; 06-04-2013 at 12:20 AM.
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