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Resources » Paper

Spencer, William Clay et al. (2009) International Worm Meeting "Genomic Strategies to Map the C. elegans Transcriptome."

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  • Comments on Spencer, William Clay et al. (2009) International Worm Meeting "Genomic Strategies to Map the C. elegans Transcriptome." (0)

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    Status:
    Publication type:
    Meeting_abstract
    WormBase ID:
    WBPaper00034137

    Spencer, William Clay, Watson, Joseph, McWhirter, Rebecca, Watkins, Kathie, Agarwal, Ashish, Gerstein, Mark, Wang, Shenglong, Kern, Nurith, & Miller III, David (2009). Genomic Strategies to Map the C. elegans Transcriptome presented in International Worm Meeting. Unpublished information; cite only with author permission.

    The C. elegans genome is completely sequenced yet many predicted genes lack biological evidence for transcription. Additionally, a substantial number of cryptic protein-coding genes and ncRNAs (miRNAs, snoRNAs, etc.) are likely to have been overlooked by gene prediction software. To identify these transcripts, we are isolating RNA from specific C. elegans cells and tissues for tiling array analysis and for high throughput cDNA sequencing (RNA-Seq). This approach ensures detection of rare RNAs from small populations of cells while also providing clues to their in vivo functions. Our data sets will be merged with complementary results from other laboratories in the modENCODE consortium (modENCODE.org) to provide a detailed picture of the C. elegans transcriptome. We use specific promoters to mark cells for isolation by FACS or for mRNA extraction by the mRNA tagging method. The small amount of RNA obtained by these methods (<25 ng) is amplified to generate a labeled ds cDNA target for hybridization to the Affymetrix C. elegans Tiling 1.0R array. To date, we have generated tiling array profiles of >20 different cells and tissues including neurons, muscle, intestine, hypodermis, excretory cell, coelomocytes, etc. Threshold analysis detects transcripts from established gene models as well as from candidate transcriptionally active regions (TARs) in intergenic and intronic domains. Biased detection of known tissue and cell-specific transcripts validates these data sets and suggests that other differentially expressed TARs may exercise cell-specific functions. In addition to detecting novel transcripts, our approach is expected to produce gene expression maps that match the single cell resolution of the C. elegans anatomy.

    Authors: Spencer, William Clay, Watson, Joseph, McWhirter, Rebecca, Watkins, Kathie, Agarwal, Ashish, Gerstein, Mark, Wang, Shenglong, Kern, Nurith, Miller III, David


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