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Homo sapiens

ABSTRACT: Genome-wide maps of H3K4me2 and DNase I hypersensitivity sites in prostate cancer cell line LNCaP and breast cancer cell line MCF-7.

PROVIDER: PRJNA149445 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR358662.fastq.gz	Fastqsanger.gz
	SRR358663.fastq.gz	Fastqsanger.gz
	SRR358664.fastq.gz	Fastqsanger.gz
	SRR358665.fastq.gz	Fastqsanger.gz
	SRR358666.fastq.gz	Fastqsanger.gz

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Homo sapiens

Project description:Genome-wide maps of H3K4me2/3 in prostate cancer cell line LNCaP

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Dual Role of FoxA1 in Androgen Receptor Binding to Chromatin, Androgen Signaling and Prostate Cancer [ChIP_seq, DHS_seq]

Project description:We report the dual role of FoxA1 in androgen receptor recruitment to the chromatin of androgen responsive prostate cancer cell line LNCaP-1F5 using ChIP-sequencing. Depletion of FoxA1 reprograms both androgen and glucocorticoid receptor recruitment and subsequent gene expression. The ChIP-seq has been performed using AR, FoxA1, GR, H3K4me2 antibodies. We have also mapped the DNaseI-hypersensitive sites (DHS) using deep sequencing. Examination of AR, FoxA1, GR, H3K4me2 binding sites and DHS sites in parental and FoxA1 depleted LNCaP-1F5 cells.

2011-09-14 | E-GEOD-30623 | biostudies-arrayexpress

Genome-wide maps of H3K4me2 and DNase I hypersensitivity sites in prostate cancer cell line LNCaP and breast cancer cell line MCF-7.

Project description:We report the high-throughput profiling of histone modification and DNase I hypersensitivity sites in prostate cancer and breaset cancer cells. We found that while AR binding is associated with nucleosome depletion, ER binding is not. We showed that a quantitative measure of DNase I hypersensitivity changes is a powerful tool in indentifying transcription factor cistromes. Examination of histone modification marked nucleosomes and Dnase I hypersensitivity in prostate cancer and breast cancer cells with and without hormone treatment.

2012-03-25 | E-GEOD-33216 | biostudies-arrayexpress

Genome-wide maps of H3K4me2 and DNase I hypersensitivity sites in prostate cancer cell line LNCaP and breast cancer cell line MCF-7.

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Genome-wide map of DNaseI hypersensitivity in mouse erythroid cells.

Project description:We generated genome-wide maps of DNaseI hypersensitivity in mouse erythroid cells by DNase-Seq.

2012-01-30 | GSE27919 | GEO

Dual Role of FoxA1 in Androgen Receptor Binding to Chromatin, Androgen Signaling and Prostate Cancer [ChIP_seq, DHS_seq]

2011-09-14 | GSE30623 | GEO

Dual Role of FoxA1 in Androgen Receptor Binding to Chromatin, Androgen Signaling and Prostate Cancer [Expression Array]

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Genome-wide map of DNaseI hypersensitivity in mouse erythroid cells.

Project description:We generated genome-wide maps of DNaseI hypersensitivity in mouse erythroid cells by DNase-Seq. Examination of DNaseI hypersensitivity in mouse erythroid cells.

2012-01-30 | E-GEOD-27919 | biostudies-arrayexpress

SPOC1 (PHF13) is a Molecular Reader and Effector of H3K4me2/3

Project description:SPOC1 is a chromatin affiliated protein with a functional role in stem cell differentiation, cell division, DNA damage response and higher order chromatin organization. To gain insight into SPOC1’s ability to modulate these processes, we elucidated the mechanisms targeting SPOC1 to chromatin and its genome wide localization. Our results demonstrate that SPOC1 binds chromatin in a multivalent fashion via its PHD domain and a centrally located domain, which interact with H3K4me2/3 and DNA, respectively. Consistently, the 3-dimensial structure of SPOC1’s PHD domain in complex with an H3K4me3 peptide could be solved. ChIP sequencing of SPOC1 in murine ES cells revealed an extensive co-occurrence with H3K4me2/3, DNAse hypersensitivity sites and Polycomb at key metabolic, cell cycle and developmental targets. Furthermore RNA sequencing demonstrated that a substantial fraction of these targets were either up or down regulated after SPOC1 depletion. Together these data identify SPOC1 as a bona fide H3K4me2/3 molecular reader and transcriptional regulator of diverse chromatin functions.

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Unbiased, Genome-wide in vivo Mapping of Transcriptional Regulatory Elements Reveals Sex Differences in Chromatin Structure Associated with Sex-specific Liver Gene Expression

Project description:We have used a simple and efficient method to identify condition-specific transcriptional regulatory sites in vivo to help elucidate the molecular basis of sex-differences in transcription, which are widespread in mammalian tissues and affect normal physiology, drug response, inflammation and disease. To systematically uncover transcriptional regulators responsible for these differences, we used DNase hypersensitivity analysis coupled with high-throughput sequencing to produce condition-specific maps of regulatory sites in male and female mouse liver, and for livers of male mice feminized by continuous infusion of growth hormone (GH). We identified 71,264 hypersensitive sites, with 1,284 showing robust sex-differences. Continuous GH infusion suppressed the vast majority of male-specific sites and induced a subset of female-specific sites in male liver. We also identified broad genomic regions (up to ~100kb) showing sex-dependent hypersensitivity and similar patterns of GH response. We found a strong association of sex-specific sites with sex-specific transcription; however, a majority of sex-specific sites were >100kb from sex-specific genes. By analyzing sequence motifs within regulatory regions, we identified two known regulators of liver sexual dimorphism, and several new candidates for further investigation. This approach can readily be applied to mapping condition-specific regulatory sites in mammalian tissues under a wide variety of physiological conditions. Global DNase Hypersensitivity in male, female, and continuous growth hormone-treated male mouse liver tissue. 10 samples: Male liver (2 replicates), Female liver (2 replicates), GH-treated male liver (2 replicates), DNase digested genomic control (from male and female liver separately) and sonicated genomic control (from male and female liver separately).

2010-09-28 | E-GEOD-21777 | biostudies-arrayexpress

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