Core14, Analysis of nascent RNA at promoters and enhancers

Description

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).

Source

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly.

RNA-seq 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

Technical Notes

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).

References

Last update: 23 Feb 2016