Schmidt 2012, CTCF binding evolution in mammals.

Description

CTCF binding evolution by comparing ChIP-seq data from six mammals.

Source

Raw data was downloaded from: ENA
Input file format: FASTQ
Download date: 19-9-2018

Samples

From M. mulatta (Nov 2015 BCM Mmul_8.0.1/rheMac8).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	ERS017357.sga	liver\|CTCF\|rep1	CTCF	-
2	ERS017348.sga	liver\|CTCF\|rep2	CTCF	-
3	ERS017376.sga	liver\|CTCF\|rep3	CTCF	-
4	ERS017353.sga	liver\|input\|rep1	input	-
5	ERS017367.sga	liver\|input\|rep2	input	-

Technical Notes

FASTQ files were mapped to the genome using Bowtie v1.1.1. SAM files were then converted to BAM using samtools v0.1.14 and to BED using bamToBed v2.27.0 (bedtools). BED to SGA conversion was carried out using bed2sga (ChIP-Seq v. 1.5.3).

References

Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A, Kutter C, Brown GD, Marshall A, Flicek P, Odom DT
Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell. 2012 Jan 20;148(1-2):335-48. doi: 10.1016/j.cell.2011.11.058. Epub 2012 Jan 12. 22244452

Last update: 1 Oct 2018