Freely/Publically available transcriptome datasets

rskr · 03-21-2012, 08:50 AM

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?

Richard Finney · 03-21-2012, 09:41 AM

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.

rskr · 03-21-2012, 09:51 AM

Quote:

Originally Posted by Richard Finney

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.

qqtwee · 07-30-2012, 11:43 PM

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!

Simon Anders · 07-31-2012, 12:14 AM

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).

davisc · 08-15-2012, 12:14 PM

ENCODE Link: http://genome-preview.ucsc.edu/cgi-b...CshlLongRnaSeq

Cheers.

Geoffreyion · 08-21-2012, 12:49 AM

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.
More info.click here.. http://www.prlog.org/12068683-ashfor...ng-40-off.html

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03-21-2012, 08:50 AM	#1
rskr Senior Member Location: Santa Fe, NM Join Date: Oct 2010 Posts: 153	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?

03-21-2012, 09:41 AM	#2
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 410	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.

08-21-2012, 12:49 AM	#7
Geoffreyion Junior Member Location: new york Join Date: Jul 2012 Posts: 6	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. More info.click here.. http://www.prlog.org/12068683-ashfor...ng-40-off.html __________________ click here >>> http://www.prlog.org/12116397-ashfor...uire-soon.html Last edited by Geoffreyion; 04-10-2013 at 10:23 PM.

07-30-2012, 11:43 PM	#4
qqtwee Member Location: Beijing Join Date: Feb 2011 Posts: 16	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!

07-31-2012, 12:14 AM	#5
Simon Anders Senior Member Location: Heidelberg, Germany Join Date: Feb 2010 Posts: 786	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).

08-15-2012, 12:14 PM	#6
davisc Junior Member Location: NYC Join Date: Oct 2008 Posts: 8	ENCODE Link: http://genome-preview.ucsc.edu/cgi-b...CshlLongRnaSeq Cheers.