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  • 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

  • #2
    Originally posted by iqc View Post
    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
    Research Scientist - Bioinformatics
    Sidra Medical and Research Center

    Comment


    • #3
      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

      Comment

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