Valouev 2008, Jurkat cells, GABP SRF NRSF.

ChIP-seq against the transcriptional activators GABP, SRF and against the transcriptional repressor NRSF (utilizing polyclonal and monoclonal antibodies) in human Jurkat cells. A negative control (input) was used.

• Raw data was downloaded from: http://mendel.stanford.edu/sidowlab/downloads/quest
• Input file format: non-standard text file format
• Download date: 14.04.2015

From H. sapiens (March 2006 NCBI36/hg18).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	gabp.sga	Jurkat GABP	GABP	-
2	srf.sga	Jurkat SRF	SRF	-
3	nrsf_poly.sga	Jurkat NRSF(polyclonal)	NRSF	-
4	nrsf_mono.sga	Jurkat NRSF(mono_clonal)	NRSF	-
5	input.sga	Jurkat input	Input	-

ChIP-seq peaks files:

	Filename	Description	Feature	GEO-ID
1	gabp_peaks.sga	Jurkat GABP peaks	GABP_P	-
2	srf_peaks.sga	Jurkat SRF peaks	SRF_P	-
3	nrsf_poly_peaks.sga	Jurkat NRSF(polyclonal) peaks	NRSF_P	-
4	nrsf_mono_peaks.sga	Jurkat NRSF(mono_clonal) peaks	NRSF_P	-

Technical Notes

The input files contain the genomic coordinates of mapped sequence tags and peak centers in a single-position format. These files were converted into SGA with ad hoc Perl scripts. The sixth field of the peak SGA files contains the value of the third field from the input files. This field is named "locmax" and apparently was used as sort field for peak ranking by the authors.

• Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A
  Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods. 2008 Sep;5(9):829-34. doi: 10.1038/nmeth.1246. 19160518