chen13, The landscape of transcription initiation in C. elegans


Sequencing of cap RNA (5'-end) of C. elebans transcripts. Samples marked as 'short' refer to nascent transcrips before they are transpliced. The scientist isolated short (20-100nt) nuclear RNA with a 5' cap from embryos. 'Long' samples are capped RNA longher than 200nt that are already transpliced and can be used to validate the 'short' samples. Original sample GSM1050559 was discarded die to very poor mapping.


Data can be downloaded from: GEO dataset GSE42819


From C. elegans genome WC190 (ce6).

Filename Description Feature GEO-ID
1 GSM1050558_short_capRNA_1.sga short cap RNA rep1 capRNA GSM1050558
2 GSM1050560_short_capRNA_2.sga short cap RNA rep2 capRNA GSM1050560
3 GSM1050561_long_capRNA_1.sga long cap RNA rep1 capRNA GSM1050561
4 GSM1050562_long_capRNA_2.sga long cap RNA rep2 capRNA GSM1050562

Technical Notes

SRA files were downloaded from GEO GSE42819 and converted in FASTQ using fastq-dump program from sratoolkit. Files marked as 'long' were paired-end (used --split-3 flag). Mapping was done using Bowtie and sam files were converted in sga files using samtools and chipseq.


  1. Chen RA, Down TA, Stempor P, Chen QB et al.
    The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures. Genome Res 2013 Aug;23(8):1339-47. PMID: 23550086

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