Additional file 2.
Table S1. EmiR expression table. smallRNA expression table as generated by the E-miR pipeline listing all expressed non-coding RNA transcripts from the annotation files that were detected in the sample data. Column description: The first column hold the transcript identifier, e.g., miRNA |ENSGALT00000028942|5p~|gga-mir-29ajsense, indicates the transcript is a miRNA with EnsemblTranscript ENSGALT00000028942 | the 5 prime part of the precursor j transcript name = gga-mir-29a and the match is the sense orientation. In cases where the miRbase has only one of the Dicer cleaved miRNA transcripts, the complementary transcripts were inferred from the hairpin structure. These unlisted transcripts are indicated by a '5p~' and '3p~' in the identifier. Expression for other non-coding RNA transcripts, like snoRNA and tRNA, are also included in the table. All of these have the '|n|' in the identifier instead of the |3/5p|. The second column holds the genome location. For each of the input files, seven columns of data are included, containing the following data: - unique: unique number of reads annotated to this miRNA transcript. - counts: sum of the number of times this miRNA transcript was found. - U0-counts: same as 'counts' but then only the sum of perfect matches only. - highest_count: expression of the most abundant isomer. - highest_seq: Identifier of the most abundant isomir: compiled from chr | begin | end | strand | mismatches in alignment | isomir sequence. - tpm scaled the 'counts' value normalized/scaled to sequences per million. - sqrt square root of the scaled value. This stabilizes variance.
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Buermans et al. BMC Genomics 2010 11:716 doi:10.1186/1471-2164-11-716