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

Description

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 http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

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.

Source

Samples

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

References

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).