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  • 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?

  • #2
    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 ...


    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, 09:44 AM.

    Comment


    • #3
      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 ...


      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.

      Comment


      • #4
        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!

        Comment


        • #5
          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).

          Comment


          • #6
            ENCODE Link: http://genome-preview.ucsc.edu/cgi-b...CshlLongRnaSeq

            Cheers.

            Comment


            • #7
              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.
              Last edited by Geoffreyion; 06-04-2013, 12:20 AM.
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