Core 2014, Analysis of nascent RNA at promoters and enhancers.

Mapping nascent RNAs purified using GRO-cap, GRO-seq and PRO-seq technologies performed in two ENCODE cells lines : human lymphoblastoid B-cell (GM12878) and chronic myelogenous leukemic (K562).

• Raw data was downloaded from GEO series: GSE60453
• Input file format: SRA

From H. sapiens (Feb 2009 GRCh37/hg19).

Transcription Profiling data:

	Filename	Description	Feature	GEO-ID
1	GSM1480321.sga	K562|GRO-cap	GRO-cap	GSM1480321
2	GSM1480323.sga	GM12878|GRO-cap	GRO-cap	GSM1480323
3	GSM1480325.sga	K562|GRO-seq	GRO-seq	GSM1480325
4	GSM1480326.sga	GM12878|GRO-seq	GRO-seq	GSM1480326
5	GSM1480327.sga	K562|PRO-Seq	PRO-Seq	GSM1480327
6	GSM1480322.sga	K562|GRO-cap control	GRO-cap	GSM1480322
7	GSM1480324.sga	GM12878|GRO-cap control	GRO-cap	GSM1480324

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the hg19 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. 1.5.2).

• Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT
  Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet. 2014 Dec;46(12):1311-20. doi: 10.1038/ng.3142. Epub 2014 Nov 10. 25383968