Chen 2013, 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.
- Raw data was downloaded
- Input file format: SRA
- Download date: n/a
From C. elegans (May 2008 WS190/ce6).
FASTQ files were extracted from SRA files using fastq-dump
toolkit v2.5.0) and mapped to the genome
using Bowtie v0.12.8. SAM
files were then converted into bam
using samtools v0.1.14
and to bed using bamToBed v2.12.0
conversion was carried out using bed2sga.pl
(ChIP-Seq v. 1.5.3).
Chen RA, Down TA, Stempor P, Chen QB, Egelhofer TA, Hillier LW, Jeffers TE, Ahringer J
The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures.
Genome Res. 2013 Aug;23(8):1339-47. doi: 10.1101/gr.153668.112. Epub 2013 Apr 2.
The landscape of RNA polymerase II transcription initiation in C. elegans reveals a novel regulatory architecture