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
Five cell lines representing cervica carcinoma, chronic myeloid leukemia, embryonic stem cells, epidermal keratinocytes, and umbilical vein endothelial cells were analyzed using ChIP-seq.
From Human Mar. 2006 (NCBI36/hg18) Assembly
|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|