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Homo sapiens

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

PROVIDER: PRJNA144937 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR326190.fastq.gz	Fastqsanger.gz
	SRR326191.fastq.gz	Fastqsanger.gz
	SRR326192.fastq.gz	Fastqsanger.gz
	SRR326193.fastq.gz	Fastqsanger.gz
	SRR326194.fastq.gz	Fastqsanger.gz

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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

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

Homo sapiens

Project description: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 [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

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.

2011-08-03 | GSE31125 | GEO

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

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Project description:Global methylation in normal and malignant urothelial cells

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EED and IgG (as control) co-immunoprecipitation of wild type embryonic stem cells (ESCs), with 3 biological replicates per condition.

Project description:DNA and Histone-3 Lysine 27 methylation typically function as repressive modifications and operate within distinct genomic compartments. In mammals, the majority of the genome is kept in a DNA methylated state, whereas the Polycomb Repressive Complexes regulate the unmethylated CpG-rich promoters of developmental genes. In contrast to this general framework, the extraembryonic lineages display non-canonical, globally intermediate DNA methylation levels that includes disruption of local Polycomb domains. To better understand this unusual landscape’s molecular properties, we genetically and chemically perturbed major epigenetic pathways in mouse Trophoblast Stem Cells (TSCs). We find that the extraembryonic epigenome reflects ongoing and dynamic de novo methyltransferase recruitment, which is continuously antagonized by Polycomb to maintain intermediate, locally disordered methylation. Despite its disorganized molecular appearance, our data point to a highly controlled equilibrium between counteracting repressors within extraembryonic cells, one that can seemingly persist indefinitely without bistable features typically seen for embryonic forms of epigenetic regulation.

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Dynamic antagonism between key repressive pathways maintains the placental epigenome -1

2023-01-27 | PXD039611 | Pride

Zebrafish 24hpf whole embryo MZezh2mutant

Project description:Polycomb group (PcG) proteins are transcriptional repressors important to maintain cell identity during embryonic development. Ezh2, the catalytic subunit of the Polycomb Repressive Complex 2, is responsible for placing the epigenetic repressive mark histone H3 lysine 27 trimethylation (H3K27me3). In contrast to results in mouse models, zebrafish embryos mutant for both maternal and zygotic ezh2 (MZezh2) can form a normal body plan at 1 day post fertilization (dpf) but die at 2 dpf, exhibiting pleiotropic phenotypes. To elucidate the specificity of PcG-mediated repression during early zebrafish development, we conducted in depth analysis of the transcriptome, epigenome, and proteome of the MZezh2 mutant embryos at 1 dpf. We found that, despite modifications in the epigenetic landscape, transcriptome and proteome analysis revealed only minor changes in gene and protein expression levels.

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