GSE25416, Genome-wide footprinting of transcription factors in human cells


Using DNaseI hypersensitivity (HS) assays (Dnase-seq), high resolution DNaseI digestion profiles were generated genome-wide in diverse human cell types. We showed that within general regions of DNaseI HS that are known to identify locations of gene regulatory elements, DNaseI digestion patterns allowed us to identify locations of individual transcription factor binding sites that protected against the bound DNA against digestion. To measure the accuracy of these footprints, we also generated ChIP-seq data for the CTCF DNA binding factor in the same cell growths. We found that DNaseI footprints containing the CTCF canonical binding motif show significant ChIP-seq signal while CTCF binding motifs not in footprints show almost no signal providing one measure of valdation of the DNaseI footprints.

For data usage terms and conditions, please refer to and

Overall design

Five cell lines representing cervica carcinoma, chronic myeloid leukemia, embryonic stem cells, epidermal keratinocytes, and umbilical vein endothelial cells were analyzed using ChIP-seq.


Files downloaded from GEO series: GSE25416
Input file format: BED


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

Filename Description Feature GEO-ID
1 GSM624077_H1_ES_UtaChIPseq_CTCF_align_rep1.sga H1_ES CTCF rep1 CTCF GSM624077
2 GSM624078_HelaS3_UtaChIPseq_CTCF_align_rep2.sga HelaS3 CTCF rep2 CTCF GSM624078
3 GSM624078_HelaS3_UtaChIPseq_CTCF_align_rep3.sga HelaS3 CTCF rep3 CTCF GSM624078
4 GSM624079_HUVEC_UtaChIPseq_CTCF_align_rep1.sga HUVEC CTCF rep1 CTCF GSM624079
5 GSM624079_HUVEC_UtaChIPseq_CTCF_align_rep2.sga HUVEC CTCF rep2 CTCF GSM624079
6 GSM624080_K562_UtaChIPseq_CTCF_align_rep1.sga K562 CTCF rep1 CTCF GSM624080
7 GSM624080_K562_UtaChIPseq_CTCF_align_rep2.sga K562 CTCF rep2 CTCF GSM624080
8 GSM624080_K562_UtaChIPseq_CTCF_align_rep3.sga K562 CTCF rep3 CTCF GSM624080
9 GSM624081_NHEK_UtaChIPseq_CTCF_align_rep1.sga NHEK CTCF rep1 CTCF GSM624081
10 GSM624081_NHEK_UtaChIPseq_CTCF_align_rep2.sga NHEK CTCF rep2 CTCF GSM624081


  1. Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS.
    High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res. 2011 Mar;21(3):456-64. PMID: 21106903.

  2. GEO series GSE25416 High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (ChIP-seq).