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The Antisense Transcriptomes of Human Cells

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Science  19 Dec 2008:
Vol. 322, Issue 5909, pp. 1855-1857
DOI: 10.1126/science.1163853
  • Table 1.

    Classification of genes with respect to antisense tags. We classified only those genes whose sum of distinct sense and antisense tags was 5 or more. S genes contained only sense tags or had a sense/antisense tag ratio of 5 or more; AS genes contained only antisense tags or had a sense/antisense tag ratio of 0.2 or less; SAS genes contained both sense and antisense tags and had a sense/antisense ratio between 0.2 and 5. Samples were derived from the following sources: PBMC, peripheral blood mononuclear cells isolated from a healthy volunteer; Jurkat, a T cell leukemia line; HCT116, a colorectal cancer cell line; MiaPaCa2, a pancreatic cancer line; MRC5, a fibroblast cell line derived from normal lung.

    Cell type
    PBMCJurkatHCT116MiaPaCa2MRC5
    No. of genes Fraction No. of genes Fraction No. of genes Fraction No. of genes Fraction No. of genes Fraction
    All genes
    S genes 10,586 81.60% 9,928 89.60% 11,176 88.00% 9,500 89.50% 10,165 89.30%
    AS genes 329 2.50% 240 2.20% 203 1.60% 155 1.50% 212 1.9%
    SAS genes 2,061 15.9% 908 8.2% 1,327 10.4% 959 9% 1,002 8.8%
    Total 12,976 11,076 12,706 10,614 11,379
    Coding genes
    S genes 10,375 81.30% 9,778 89.50% 10,770 87.60% 9,348 89.40% 10,029 89.20%
    AS genes 325 2.50% 239 2.20% 201 1.60% 154 1.50% 210 2%
    SAS genes 2,055 16.1% 907 8.3% 1,325 10.8% 959 9.2% 1,000 8.9%
    Total 12,755 10,924 12,296 10,461 11,239
    Noncoding genes
    S genes 211 95.50% 150 98.70% 406 99.00% 152 99.30% 136 97.10%
    AS genes 4 1.80% 1 0.70% 2 0.50% 1 0.70% 2 1.4%
    SAS genes 6 2.7% 1 0.70% 2 0.50% 0 0% 2 1.4%
    Total 221 152 410 153 140

Additional Files


  • The Antisense Transcriptomes of Human Cells
    Yiping He, Bert Vogelstein, Victor E. Velculescu, Nickolas Papadopoulos, Kenneth W. Kinzler

    Supporting Online Material

    This supplement contains:
    Materials and Methods
    Figs. S1 to S13
    References

    This file is in Adobe Acrobat PDF format.

    Other Supporting Online Material for this manuscript includes the following:

    Tables S1 to S3. Data tables supporting study, presented in Microsoft Excel format. Excel files are packaged as a compressed archive, in *.zip format; users should download the compressed file to their machine and decompress the file on their local hard drive, using the instructions below.

    Table S1: Summary of tags used in study.
    Table S2: ASSAGE profiles for 32,354 Ensembl genes.
    Table S3: Genes with predominantly antisense tags in one cell type and predominantly sense tags in another cell type.


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