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 from: GEO
• Input file format: SRA
• Download date: n/a

From C. elegans (May 2008 WS190/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

FASTQ files were extracted from SRA files using fastq-dump (SRA 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 (bedtools). SGA 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. 23550086
• GEO series GSE42819: The landscape of RNA polymerase II transcription initiation in C. elegans reveals a novel regulatory architecture