public paire end (mate pair) transcriptome data set?

iqc · 08-26-2009, 03:51 PM

Hi All,

Does anyone know a public data set that has paired-ends (mate pair) and is on the transcriptome? If I browse a public database such as the NCBI short reads, how can I find out whether a data set has paired ends? Are there other public databases to look?

Thanks,

xq

ramouz87 · 11-12-2009, 03:07 AM

Quote:

Originally Posted by iqc

Hi All,

Does anyone know a public data set that has paired-ends (mate pair) and is on the transcriptome? If I browse a public database such as the NCBI short reads, how can I find out whether a data set has paired ends? Are there other public databases to look?

Thanks,

xq

Hi xq,
have you find such dataset ? I looking for that too.
i would be thankfull if you could let me know
thanks uin advance,
Regards,
Ramzi

Chien-Yuan Chen · 11-12-2009, 01:18 PM

GEO data GSE 13652
Expression profiling by high throughput sequencing
We carried out the first analysis of alternative splicing complexity in human tissues using mRNA-Seq data. New splice junctions were detected in 20% of multiexon genes, many of which are tissue specific. By combining mRNA-Seq and EST-cDNA sequence data, we estimate that transcripts from 95% of multiexon genes undergo alternative splicing and that there are 100,000 intermediate- to high-abundance alternative splicing events in major human tissues. From a comparison with quantitative alternative splicing microarray profiling data, we also show that mRNA-Seq data provide reliable measurements for exon inclusion levels.

Keywords: mRNA expression

Overall design 32-nucleotide sequence reads from six human tissues including brain, cerebral cortex, heart, liver, lung and skeletal muscle.

Contributor(s) Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ
Citation(s) 18978789
Pan Q, Shai O, Lee LJ, Frey BJ et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008 Dec;40(12):1413-5. PMID: 18978789

Submission date Nov 18, 2008
Contact name Weijun Gao
Organization name University of Toronto

Street address 10 King's College Rd.

City Toronto
ZIP/Postal code M5S 3G4
Country Canada

Platforms (1) GPL9052 Illumina Genome Analyzer (Homo sapiens)

Samples (6)
Less...
More... GSM343511 brain
GSM343512 cerebral cortex
GSM343513 heart

GSM343514 liver
GSM343515 lung
GSM343516 skeletal muscle

Download family Format
SOFT formatted family file(s) SOFT
MINiML formatted family file(s) MINiML
Series Matrix File(s) TXT

Supplementary file Size Download File type/resource
GSE13652_RAW.tar 2.7 Gb (ftp)(http) TAR (of TXT)
SRP000/SRP000626 (ftp) SRA Study
Raw data not provided for this record
Processed data provided as supplementary file

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08-26-2009, 03:51 PM	#1
iqc Junior Member Location: US Join Date: Aug 2009 Posts: 1	public paire end (mate pair) transcriptome data set? Hi All, Does anyone know a public data set that has paired-ends (mate pair) and is on the transcriptome? If I browse a public database such as the NCBI short reads, how can I find out whether a data set has paired ends? Are there other public databases to look? Thanks, xq

11-12-2009, 01:18 PM	#3
Chien-Yuan Chen Member Location: USA Join Date: Feb 2009 Posts: 19	GEO data GSE 13652 Expression profiling by high throughput sequencing We carried out the first analysis of alternative splicing complexity in human tissues using mRNA-Seq data. New splice junctions were detected in 20% of multiexon genes, many of which are tissue specific. By combining mRNA-Seq and EST-cDNA sequence data, we estimate that transcripts from 95% of multiexon genes undergo alternative splicing and that there are 100,000 intermediate- to high-abundance alternative splicing events in major human tissues. From a comparison with quantitative alternative splicing microarray profiling data, we also show that mRNA-Seq data provide reliable measurements for exon inclusion levels. Keywords: mRNA expression Overall design 32-nucleotide sequence reads from six human tissues including brain, cerebral cortex, heart, liver, lung and skeletal muscle. Contributor(s) Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ Citation(s) 18978789 Pan Q, Shai O, Lee LJ, Frey BJ et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008 Dec;40(12):1413-5. PMID: 18978789 Submission date Nov 18, 2008 Contact name Weijun Gao Organization name University of Toronto Street address 10 King's College Rd. City Toronto ZIP/Postal code M5S 3G4 Country Canada Platforms (1) GPL9052 Illumina Genome Analyzer (Homo sapiens) Samples (6) Less... More... GSM343511 brain GSM343512 cerebral cortex GSM343513 heart GSM343514 liver GSM343515 lung GSM343516 skeletal muscle Download family Format SOFT formatted family file(s) SOFT MINiML formatted family file(s) MINiML Series Matrix File(s) TXT Supplementary file Size Download File type/resource GSE13652_RAW.tar 2.7 Gb (ftp)(http) TAR (of TXT) SRP000/SRP000626 (ftp) SRA Study Raw data not provided for this record Processed data provided as supplementary file