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.



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

Technical Notes

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 (ChIP-Seq v. 1.5.3).


Last update: 1 Oct 2018