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Integrated epigenome profiling of repressive histone modifications, DNA methylation and gene expression in normal and malignant urothelial cells [ChIP-Seq data]

ABSTRACT: We profiled two repressive histone modifications (H3K9m3 and H3K27m3) using ChIP-Seq in normal urothelial cells and cell lines representing non-invasive and invasive tumors.

ORGANISM(S): Homo sapiens

PROVIDER: GSE31125 | GEO | 2011/08/03

SECONDARY ACCESSION(S): PRJNA144937

REPOSITORIES: GEO

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Integrated epigenome profiling of repressive histone modifications, DNA methylation and gene expression in normal and malignant urothelial cells [ChIP-Seq data]

Project description:We profiled two repressive histone modifications (H3K9m3 and H3K27m3) using ChIP-Seq in normal urothelial cells and cell lines representing non-invasive and invasive tumors. Two bladder cancer cell lines (RT112 and EJ/T24 from ATCC) and normal human urothelial (NHU) cells were treated according to standard ChIP-Seq protocols using antibodies against the histone modifications H3K9m3 and H3K27m3 (from Millipore). The sequencing reads were mapped against the human genome (GRCh37/hg19).

2011-08-03 | E-GEOD-31125 | biostudies-arrayexpress

Epigenome profiling of repressive histone modifications, DNA methylation and gene expression in normal and malignant urothelial cells

Project description:To gain a more depth knowledge of repressive epigenetic gene regulation in UCC, we have profiled H3K9m3 and H3K27m3 in normal and malignant urothelial cells. We matched these profiles to those 5-methylcytosine and gene expression. We hypothesized that differences represent pro-carcinogenic events within the urothelium. We identified a panel of genes with cancer specific epigenetic mediated aberrant expression. Two repressive histone modifications (H3K9m3 and H3K27m3) , cytosine methylation and gene expression were compared between normal human urothelial cell line (NHU) and malignant urothelial cells (EJ and RT112).

2011-09-19 | E-GEOD-31864 | biostudies-arrayexpress

Epigenome profiling of repressive histone modifications, DNA methylation and gene expression in normal and malignant urothelial cells

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Integrated epigenome profiling of repressive histone modifications, DNA methylation and gene expression in normal and malignant urothelial cells.

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Integrated epigenome profiling of DNA methylation and gene expression in normal and malignant urothelial cells

Project description:This SuperSeries is composed of the following subset Series: GSE31864: Epigenome profiling of repressive histone modifications, DNA methylation and gene expression in normal and malignant urothelial cells GSE31865: Global methylation in normal and malignant urothelial cells Refer to individual Series

2011-09-19 | E-GEOD-31866 | biostudies-arrayexpress

Tobacco smoking transcriptional imprinting contributes to urothelial cancer

Project description:Smoking is a major risk factor for Urothelial carcinoma (UC). However the complex mechanisms, how smoking promotes carcinogenesis and tumour progression, remain obscure. A microarray based approached was therefore performed to detect the smoking derived gene expression alteration in non-malignant and malignant urothelial tissues from patients with superficial or invasive UC. Smoking enhanced cell migration and response to tissue damages. In non-malignant tissues smoking induced immune response and altered the cytoskeleton. In urothelial carcinoma, smoking altered extracellular and chromosome structures. Smoking affected tissues from patients with invasive carcinomamore strongly, up-regulating particularly growth factors and oncogenes in non-malignant tissue of patients with invasive but not with superficial carcinoma. In former smokers, comparable changes were seen in tissues form patients with invasive disease while they were minor or reversed in tissue of patients with superficial disease. Best but not complete tissue repair was suggestedfor non-malignant tissue from patients with superficial tumours. we used microarray techniques to define gene expression profile which may explain the contribution of smoking to urothelial carcinoma. Gene expression profiling using GeneChip HG-U133A Plus 2.0 (Affymetrix) was performed on non-malignant and carcinogenic urothelium from six patients with superficial and six with invasive urothelial carcinoma, each group including two current, former, and non-smokers.

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Tobacco smoking transcriptional imprinting contributes to urothelial cancer

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Global methylation in normal and malignant urothelial cells

Project description:We have created 5-methylcytosine profiles for normal and malignant urothelial cells.

2011-09-20 | GSE31865 | GEO

Methyltransferase Inhibitors Restore SATB1 Protective Activity Against Cutaneous T cell Lymphoma

Project description:We report Chromatin Immunoprecipitation for the histone modifications H3K27ac, H3K27m3 and H3K9m3 in human leukemia and lymphoma cell lines HuT78, Jurkat, K562, and RAJI to ascertain the regulatory landscape of in regards to transcriptional repression and activation.

2022-10-26 | GSE159962 | GEO

Global methylation in normal and malignant urothelial cells

Project description:We have created 5-methylcytosine profiles for normal and malignant urothelial cells. Competitive hybridization of background and 5-methylcytosine enriched immunoprecipiated DNA fractions

2011-09-19 | E-GEOD-31865 | biostudies-arrayexpress

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