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Series GSE20042 Query DataSets for GSE20042
Status Public on Mar 09, 2010
Title Genome-wide maps of H3K4me2/3 in prostate cancer cell line LNCaP
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We report the high-throughput profiling of histone modifications in prostate cancer cells. By obtaining over 1 billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of prostate cancer cells. we found androgen treatment dismisses a nucleosome over AR binding sites that are flanked by a pair of H3K4me2 marked nucleosomes. A novel quantitative model built on the behavior of such nucleosome pairs correctly identified regions bound by the regulators of the immediate androgen response including AR and FoxA1. More importantly this model also correctly predicted novel binding sites for other transcription factors present following prolonged androgen stimulation including Oct1 and NKX3.1. Thus quantitative modeling of enhancer structure provides a powerful predictive method to infer the identity of transcription factors involved in cellular responses to specific stimuli.
Overall design Examination of 2 different histone modifications in prostate cancer cells with and without androgen (dihydrotestosterone, DHT) treatment.
Contributor(s) He HH, Meyer CA, Brown M, Liu XS
Citation(s) 20208536
Submission date Jan 26, 2010
Last update date May 15, 2019
Contact name Housheng Hansen He
Phone 617-632-4738
Organization name Dana-Farber Cancer Institute
Department Medical Oncology
Lab Myles Brown
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (5)
GSM503903 H3K4me2_Vehicle_ChIPSeq
GSM503904 H3K4me2_DHT_4h_ChIPSeq
GSM503905 H3K4me2_DHT_16h_ChIPSeq
SRA SRP002077
BioProject PRJNA124303

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Supplementary file Size Download File type/resource
GSE20042_RAW.tar 244.7 Mb (http)(custom) TAR (of BED, TXT)
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Processed data provided as supplementary file
Raw data are available in SRA

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