Transcriptomics

Dataset Information

0

FAIRE-chip in MCF7 and LNCaP


ABSTRACT: The compaction degree of chromatin is intimately related to its functionality and active cis-regulatory elements typically exist within open chromatin regions depleted in nucleosomes (Heintzman et al. 2007; Boyle et al. 2008). These domains can be identified using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) that allows for enrichment of nucleosome-depleted genomic regions when cross-linked chromatin is subjected to phenol-chloroform extraction (Nagy et al. 2003; Hogan et al. 2006) Here, chromatin structure was analyzed in MCF7 and LNCaP cells using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Nagy et al. 2003; Hogan et al. 2006) Keywords: FAIRE-chip MCF7 and LNCaP cells were grown in full media, cross-linked and processed as in (Nagy et al. 2003; Hogan et al. 2006). DNA obtained by FAIRE was hybridized to Human Affymetrix tiled array F. Triplicates of FAIRE and input DNA are provided (4 inputs for MCF7 cells).

ORGANISM(S): Homo sapiens  

SUBMITTER: Jérôme Eeckhoute   

PROVIDER: E-GEOD-11579 | ArrayExpress | 2010-05-14

SECONDARY ACCESSION(S): GSE11579PRJNA106209

REPOSITORIES: GEO, ArrayExpress

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Publications

Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers.

Eeckhoute Jérôme J   Lupien Mathieu M   Meyer Clifford A CA   Verzi Michael P MP   Shivdasani Ramesh A RA   Liu X Shirley XS   Brown Myles M  

Genome research 20090107 3


Selective activity of a specific set of enhancers defines tissue-specific gene transcription. The pioneer factor FOXA1 has been shown to induce functional enhancer competency through chromatin openings. We have previously found that FOXA1 is recruited to thousands of regions across the genome of a given cell type. Here, we monitored the chromatin structure at FOXA1 binding sites on a chromosome-wide scale using formaldehyde assisted isolation of regulatory elements (FAIRE). Surprisingly, we find  ...[more]

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