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Homo sapiens

ABSTRACT: ChIP-seq-based analysis of differential K27me3 coverage in neuroblastoma cell lines treated with epigenetic drugs

PROVIDER: PRJNA318912 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3402850.fastq.gz	Fastqsanger.gz
	SRR3402851.fastq.gz	Fastqsanger.gz
	SRR3402852.fastq.gz	Fastqsanger.gz
	SRR3402843.fastq.gz	Fastqsanger.gz
	SRR3402853.fastq.gz	Fastqsanger.gz

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ChIP-seq-based analysis of i) K27me3 promoter coverage and ii) enhancer elements in neuroblastoma cell lines

Project description:To investigate whether a set of differentially methylated/expressed genes, identified in neuroblastomas of differential outcome, co-localizes with K27me3 marks or enhancer elements, we performed H3K4me3, H3K4me1, H3K27ac and H3K27me3 ChIP seq in neuroblastoma cell lines.

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ChIP-seq-based analysis of differential K27me3 coverage in neuroblastoma cell lines treated with epigenetic drugs

Project description:The impact of drugs inhibiting DNA methylation (5-aza-2'-deoxycytodine, DAC) and EZH2 (EPZ-6438) on H3K27me3 coverage was analyzed in two neuroblastoma cell lines. Parallel analyses investigated associated changes in RNA expression and DNA methylation. The neuroblastoma cell lines Be(2)-C and IMR5-75 were treated with a combination of DAC and EPZ-6438. Controls were treated with solvent (DMSO). H3K27me3 ChIP seq was done to investigate treatment-related changes of this mark. In addition, H3K4me3 and H3K27ac ChIP seq was done in DMSO treated samples to identify putative regulatory regions.

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Project description:ChIP-seq-based analysis of i) K27me3 promoter coverage and ii) enhancer elements in neuroblastoma cell lines

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Project description:RNA expression analysis of neuroblastoma cell lines treated with epigenetic drugs

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Project description:DNA methylation analysis of neuroblastoma cell lines treated with epigenetic drugs

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ChIP-seq-based analysis of differential K27me3 coverage in neuroblastoma cell lines treated with epigenetic drugs

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Differential gene expression analysis of pediatric acute myeloid leukemia cell lines treated with azacytidine and panobinostat alone or in combination and compared to vehicle treated cells.

Project description:Pediatric AML cell lines (MV4;11, AML-193 and THP-1) were treated with DNA hypomethylating agent (azacytidine) and a pan histone deactylase inhibitor (panobinostat) alone or in combination. Treatment of AML cell lines with these epigenetic drugs synergistically suppresses cell viability in vitro and in xenograft models in vivo. Data show differential regulation of gene expression in AML cell lines by epigenetic drugs at concentrations which retained cell viability at a minimum of 75% even in the combination treatment.

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RNA expression analysis of neuroblastoma cell lines treated with epigenetic drugs

Project description:The impact of drugs inhibiting DNA methylation (5-aza-2'-deoxycytodine, DAC) and EZH2 (EPZ-6438) on the neuroblastoma transcriptome was analyzed in two neuroblastoma cell lines. Parallel analyses investigated associated changes in histone modification and DNA methylation. The neuroblastoma cell lines Be(2)-C and IMR5-75 were treated with DAC and EPZ-6438 in combination or alone. Controls were treated with solvent (DMSO). RNA was isolated and sequenced.

2016-09-08 | E-GEOD-79859 | biostudies-arrayexpress

DNA methylation analysis of neuroblastoma cell lines treated with epigenetic drugs

Project description:The impact of drugs inhibiting DNA methylation (5-aza-2'-deoxycytodine, DAC) and EZH2 (EPZ-6438) on the neuroblastoma methylome was analyzed in two neuroblastoma cell lines. Parallel analyses investigated associated changes in histone modification and RNA expression. The neuroblastoma cell lines Be(2)-C and IMR5-75 were treated with a combination of DAC and EPZ-6438. Controls were treated with solvent (DMSO). DNA was isolated, bisulphite converted and hybridised to the llumina HumanMethylation450 BeadChip

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Project description:Neuroblastoma cell lines are an important and cost-effective model used to study oncogenic drivers of the disease. While many of these cell lines have been previously characterized with SNP, methylation, and/or expression microarrays, there has not been an effort to comprehensively sequence these cell lines. Here, we present raw whole transcriptome data generated by RNA sequencing of 39 commonly-used neuroblastoma cell lines. This data can be used to perform differential expression analysis based on a genetic aberration or phenotype in neuroblastoma (eg: MYCN amplification status, ALK mutation status, 11q status, sensitivity to pharmacological pertubation). Additionally, we designed this experiment to enable structural variant and/or long-noncoding RNA analysis across these cell lines. Finally, as more DNase/ATAC and histone/transcription factor ChIP sequencing is performed in these cell lines, our RNA-Seq data will be an important complement to inform transcriptional targets as well as regulatory (enhancer or repressor) elements in neuroblastoma.

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