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High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

ABSTRACT: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE25442 | GEO | 2010/11/18

REPOSITORIES: GEO

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High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

Project description:This SuperSeries is composed of the following subset Series: GSE25344: High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (Dnase-seq) GSE25416: High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (ChIP-seq) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Refer to individual Series

2010-11-18 | E-GEOD-25442 | biostudies-arrayexpress

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (ChIP-seq)

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

2010-11-18 | E-GEOD-25416 | biostudies-arrayexpress

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (Dnase-seq)

Project 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 Six cell lines representing cervica carcinoma, chronic myeloid leukemia, human embryonic stem cells, lymphoblastoid cells, human epidermal keratinocytes and umbilical vein endothelial cells were analyzed using Dnase-seq.

2010-11-18 | E-GEOD-25344 | biostudies-arrayexpress

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (Dnase-seq)

2010-11-18 | GSE25344 | GEO

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (ChIP-seq)

2010-11-18 | GSE25416 | GEO

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.

Project description:Regulation of gene transcription in diverse cell types is determined largely by varied sets of cis-elements where transcription factors bind. Here we demonstrate that data from a single high-throughput DNase I hypersensitivity assay can delineate hundreds of thousands of base-pair resolution in vivo footprints in human cells that precisely mark individual transcription factor-DNA interactions. These annotations provide a unique resource for the investigation of cis-regulatory elements. We find that footprints for specific transcription factors correlate with ChIP-seq enrichment and can accurately identify functional versus nonfunctional transcription factor motifs. We also find that footprints reveal a unique evolutionary conservation pattern that differentiates functional footprinted bases from surrounding DNA. Finally, detailed analysis of CTCF footprints suggests multiple modes of binding and a novel DNA binding motif upstream of the primary binding site.

| S-EPMC3044859 | biostudies-other

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

Project description:For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf This SuperSeries is composed of the SubSeries listed below.

2011-10-18 | GSE32883 | GEO

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

Project description:This SuperSeries is composed of the following subset Series: GSE19622: Individual-specific and allele-specific chromatin signatures in diverse human populations GSE25416: High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (ChIP-seq) GSE30226: Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity [ChIP_seq]. GSE32692: Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells [new ChIP-Seq samples] For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Refer to individual Series

2011-10-17 | E-GEOD-32883 | biostudies-arrayexpress

High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq.

Project description:Accurate identification of the DNA-binding sites of transcription factors and other DNA-binding proteins on the genome is crucial to understanding their molecular interactions with DNA. Here, we describe a new method: Genome Footprinting by high-throughput sequencing (GeF-seq), which combines in vivo DNase I digestion of genomic DNA with ChIP coupled with high-throughput sequencing. We have determined the in vivo binding sites of a Bacillus subtilis global regulator, AbrB, using GeF-seq. This method shows that exact DNA-binding sequences, which were protected from in vivo DNase I digestion, were resolved at a comparable resolution to that achieved by in vitro DNase I footprinting, and this was simply attained without the necessity of prediction by peak-calling programs. Moreover, DNase I digestion of the bacterial nucleoid resolved the closely positioned AbrB-binding sites, which had previously appeared as one peak in ChAP-chip and ChAP-seq experiments. The high-resolution determination of AbrB-binding sites using GeF-seq enabled us to identify bipartite TGGNA motifs in 96% of the AbrB-binding sites. Interestingly, in a thousand binding sites with very low-binding intensities, single TGGNA motifs were also identified. Thus, GeF-seq is a powerful method to elucidate the molecular mechanism of target protein binding to its cognate DNA sequences.

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Individual-specific and allele-specific chromatin signatures in diverse human populations

Project description:This dataset contains DNase-seq data and CTCF ChIP-seq data for 6 lymphoblastoid cell lines. There are 3 cell lines from a YRI trio and 3 lines from a CEU trio (HapMap GM19238, GM19239, GM 19240, GM12891, GM12892, GM12878). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf DNase-seq and ChIP-seq data from each of the 6 cell lines.

2010-03-15 | E-GEOD-19622 | biostudies-arrayexpress

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