Schmidt 2012, CTCF binding evolution in mammals.

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

• Raw data was downloaded from: ENA
• Input file format: FASTQ
• Download date: 3-4-2018

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	ERS017350.sga	liver|CTCF|rep1	CTCF	-
2	ERS017374.sga	liver|CTCF|rep2	CTCF	-
3	ERS066527.sga	liver|NRSF	NRSF	-
4	ERS017369.sga	liver|input|rep1	input	-
5	ERS017358.sga	liver|input|rep2	input	-

FASTQ were mapped to the genome using Bowtie v0.12.8. SAM files were then converted to 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. 1.5.3).

• 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