Genomics

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ChIP-Seq analysis of ER binding sites in MCF7 breast cancer cells


ABSTRACT: Estrogen Receptor (ER) is a hormonal transcription factor that plays important roles in breast cancer. It functions primarily through binding to the regulatory regions of target genes containing the consensus ERE motifs. In order to identify ER target genes and re-define the ERE motifs we performed ChIP-Seq analysis of ER in MCF7 breast cancer cell line. Applying a novel computational algorithm named Hybrid Motif Sampler (HMS), specifically designed for TFBS motif discovery in ChIP-Seq data, we were able to detect an improved ERE motif and reveal intra-motif dependency especially in neighboring base pairs. MCF7 cells were grown in starving medium (RPMI with 5% FCS) for 3 days prior to the treatment with 10 nM β-estradiol or vehicle control for 45 minutes. ChIP was done using an anti-ER antibody in both the ethl-treated and the E2-treated cells. ChIP-Seq sample prep and sequencing were done following the manufacture's protocol using the Genome Analyzer (Illumina). The read files were analyzed using ethl-treated as control for E2-treated, leading to one final peak file.

ORGANISM(S): Homo sapiens  

SUBMITTER: Jindan Yu   Arul M Chinnaiyan 

PROVIDER: E-GEOD-19013 | ArrayExpress | 2010-02-01

SECONDARY ACCESSION(S): GSE19013SRP001836PRJNA121079

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

On the detection and refinement of transcription factor binding sites using ChIP-Seq data.

Hu Ming M   Yu Jindan J   Taylor Jeremy M G JM   Chinnaiyan Arul M AM   Qin Zhaohui S ZS  

Nucleic acids research 20100106 7


Coupling chromatin immunoprecipitation (ChIP) with recently developed massively parallel sequencing technologies has enabled genome-wide detection of protein-DNA interactions with unprecedented sensitivity and specificity. This new technology, ChIP-Seq, presents opportunities for in-depth analysis of transcription regulation. In this study, we explore the value of using ChIP-Seq data to better detect and refine transcription factor binding sites (TFBS). We introduce a novel computational algorit  ...[more]

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