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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE17768: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: gene expression GSE17769: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: DNA methylation GSE21347: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: allelic status GSE21540: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: CGH Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Raj Chari

PROVIDER: E-GEOD-21541 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: CGH

Project description:This study was undertaken to identify novel tumour suppressor genes in lung adenocarcinoma. EYA4, located at 6q23.2 was identified as a frequently lost and hypermethylated gene in the analyzed samples. 7 Breast cancer cell lines profiled on the SMRTr array in conjunction with matched DNA methylation data, allelic status and gene expression data for integrative analysis.

2010-12-31 | E-GEOD-21540 | biostudies-arrayexpress

EYA4 is a non-small cell lung cancer tumor suppressor located in the susceptibility locus on chromosome 6q

Project description:This study was undertaken to identify novel tumour suppressor genes in lung adenocarcinoma. EYA4, located at 6q23.2 was identified as a frequently lost and hypermethylated gene in the analyzed samples. EYA4 is underexpressed in addition to being deleted and hypermethylated. Control of EYA4 expression by DNA methylation was assessed using 5'-azacytidine. The role of EYA4 in apoptosis was assessed using a stable knock down of the gene which was assessed for apoptotis using FACS and qPCR. Methylation profiling: 30 adenocarcinoma samples and 30 patient-matched non-malignant lung samples are included. Non-malignant samples were used as references to identify hypermethylated probes. For each normal/tumor pair, the sample numbers are paired but offset by one with the tumor being the lower of the two numbers. For example, 85040001 is the adenocarcinoma tumor profile that pairs with non-malignant 85040002. Genome variation (aCGH) profiling: 30 adenocarcinoma gene dosage profiles are included. Values presented are log2 ratios of Cy3(sample)/Cy5(diploid reference)

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Project description:An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer

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INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA

Project description:This SuperSeries is composed of the following subset Series: GSE35082: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (expression) GSE35329: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (SNP data) GSE35367: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (CGH) Refer to individual Series

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Variegated gene expression caused by cell-specific long-range DNA interactions

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2011-06-15 | E-GEOD-24614 | biostudies-arrayexpress

ChIP-chip analysis of HTZ-1 and RNA Polymerase II in wildtype (N2) embryos

Project description:In all eukaryotes, histone variants are incorporated into a subset of nucleosomes to create functionally specialized regions of chromatin. One such variant, H2A.Z, replaces histone H2A and is required for viability in all metazoans tested to date. However, the function of H2A.Z in chromatin organization, transcription, and development remains controversialunclear. We mapped the genome-wide distribution of the C. elegans H2A.Z ortholog HTZ-1 during embryogenesis by Chromatin ImmunoPrecipitation on DNA microarrays (ChIP-chip). We find that H2A.Z is incorporated upstream of approximatelybout 25% of C. elegans genes, preferentially upstream of genes required for development and occupied by RNA polymerase II. Fewer sites of HTZ-1 localization occur on the X chromosome relative to autosomes, consistent with the lack of essential genes on X. The data provide evidence for unexpectedly widespread independent regulation of genes within operons. In 37% of operons, HTZ-1 is incorporated upstream of internally encoded genes. In conjunction with ChIP-chip, we used genetic mutation, RNAi, and microscopy to establish that HTZ-1 is present in every cell, and that maternally supplied HTZ-1 is essential for normal development. We interpret these results to indicate that C. elegans HTZ-1 functions in establishing or maintaining an essential chromatin state at promoters regulated dynamically during development. Keywords: chip-chip 4 independent HTZ-1 ChIP biological replicates were performed with 1 dye-swap replicate (ChIP 4). RNA Polymerase II ChIPs were performed from extracts used for HTZ-1 ChIPs 1 and 2 (RNAPII ChIP2 is a dye-swap). HTZ-1, RNA Polymerase II, and no antibody raw intensities Data were normalized by median centering log ratios (IP/input). Normalized Log2 ratios from each experiment were converted to standardized z-scores, array sets were concatenated, and then the median of experiments was taken.

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