Schmidt 2012, CTCF binding evolution in mammals.

Description

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

Source

Samples

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 -

Technical Notes

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).

References

Last update: 3 Apr 2018