Yan 2013, Large collection of transcription factors profiling in LoVo cells
Description
ChIP-seq in LoVo cells against highly expressed tanscription factors, CTCF, modified and variant histones, p300,
subunits of cohesin (SMC1A, SMC3, and RAD21), the cohesin loading factor NIPBL and mediator subunits (MED1, MED12).
LoVo is a human colon adenocarcinoma cell line. IgG used as control.
Source
Raw data was downloaded from from GEO series:
GSE49402
Low quality samples are marked with "FailedQC" term whereas high quality samples are marked with "PassedQC".
Technical Notes
FASTQ files were extracted from SRA files using fastq-dump
(SRA
toolkit v2.5.0) and mapped to the hg 19 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).
BED files were lifted over to hg18 assembly using liftOver. SGA conversion was carried out using bed2sga.pl
(ChIP-Seq v. 1.5.2).
Peak files were converted to SGA format using in-house software.
References
Yan J, Enge M, Whitington T, Dave K, Liu J, Sur I, Schmierer B, Jolma A, Kivioja T, Taipale M, Taipale J
Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites.
Cell. 2013 Aug 15;154(4):801-13. doi: 10.1016/j.cell.2013.07.034.
23953112
GEO series GSE49402:
Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites.