Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA122647 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The Human Genome Project promised to promote large-scale functional analyses necessary for the diagnosis and treatment of complex diseases. Here we demonstrate an integrated approach to the study of a transcriptional regulatory cascade involved in the progression of breast cancer and we identify a protein associated with disease progression. Using chromatin immunoprecipitation and genome tiling arrays, whole genome mapping of transcription factor binding sites was combined with gene expression profiling to identify genes involved in the proliferative response to estrogen (E2). Using RNA interference, selected ERa and c-Myc gene targets were knocked down to identify mediators of E2-stimulated cell proliferation. Tissue microarray screening revealed that high expression of an epigenetic factor, the estrogen-inducible histone variant H2A.Z, is significantly associated with lymph node metastasis and decreased breast cancer survival. Detection of H2A.Z levels independently increased the prognostic power of biomarkers currently in clinical use. This integrated approach has accelerated the identification of a molecule linked to breast cancer progression, has implications for diagnostic and therapeutic interventions, and can be applied to a wide range of cancers. Keywords: treated vs. untreated
2008-02-28 | GSE10618 | GEO
Project description:The Human Genome Project promised to promote large-scale functional analyses necessary for the diagnosis and treatment of complex diseases. Here we demonstrate an integrated approach to the study of a transcriptional regulatory cascade involved in the progression of breast cancer and we identify a protein associated with disease progression. Using chromatin immunoprecipitation and genome tiling arrays, whole genome mapping of transcription factor binding sites was combined with gene expression profiling to identify genes involved in the proliferative response to estrogen (E2). Using RNA interference, selected ERa and c-Myc gene targets were knocked down to identify mediators of E2-stimulated cell proliferation. Tissue microarray screening revealed that high expression of an epigenetic factor, the estrogen-inducible histone variant H2A.Z, is significantly associated with lymph node metastasis and decreased breast cancer survival. Detection of H2A.Z levels independently increased the prognostic power of biomarkers currently in clinical use. This integrated approach has accelerated the identification of a molecule linked to breast cancer progression, has implications for diagnostic and therapeutic interventions, and can be applied to a wide range of cancers. MCF7 cells treated with E2 (10nM) or Ctrl (vehicle) for 4, 12 or 24 hours. Each hormone treatment time was performed at least three times and hybridizations included dye swaps.
2010-06-25 | E-GEOD-10618 | biostudies-arrayexpress
Project description:Transcriptome of lsm8-1 mutant using whole genome tiling arrays
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Project description:Recent advances in multiple whole genome technologies provide unprecedented opportunities to profile epigenomic signatures in cancer cells. Previously we used a human gene promoter tiling microarray platform to identify genome-wide DNA methylation changes in a cell line model of breast cancer metastasis. Interestingly, the clustered nature of epigenetic targets that we identified, along with our concurrent karyotype analyses, have now led us to hypothesize that complex genomic alterations in cancer cells (deletions, translocations and ploidy) may be superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes. This SuperSeries is composed of the SubSeries listed below.
2009-07-03 | GSE15619 | GEO
Project description:Transcript Mapping on Affymetrix ENCODE arrays for 3 different biological replicates of Placental Poly(A)+ RNA (each with either 2 or 3 technical replicates) Keywords = Transcript Mapping, Human, Affymetrix, Genome Tiling Arrays Keywords: other
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Project description:Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole genome tiling arrays
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Project description:Transcript Mapping on Affymetrix ENCODE arrays for 10 different biological replicates of Neutrophil (PMN) Total RNA (each with 2 technical replicates). Each biological sample is from a different individual. Keywords = Transcript Mapping, Human, Affymetrix, Genome Tiling Arrays Keywords: other
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Project description:We have used a human gene promoter tiling microarray platform to analyze a cell line model of lymph node metastasis comprised of a poorly metastatic MDA-MB-468GFP human breast adenocarcinoma cell line and its highly metastatic variant (468LN). Gene networks and pathways associated with metastasis were identified and target genes associated with epithelial-mesenchymal transition (EMT) was validated with respect to DNA methylation effects on gene expression. We integrated data from the tiling microarrays with targets identified by Ingenuity Pathway Analysis software and observed epigenetic variations in genes implicated in EMT and with tumor cell migration. We identified widespread genomic hyper- and hypo- methylation events in these cells and we confirmed functional associations between methylation status and expression of the CDH1, CST6, EGFR, SNAI2 and ZEB2 genes by quantitative RealTime PCR. Our data also suggest that the complex genomic reorganization present in cancer cells may be superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes. Keywords: Lymph node metastatic vs non metastatic
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Project description:Mapping of in vivo Heat Shock Factor binding sites in drosophila embryos with genomic tiling arrays Keywords: repeat sample
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Project description:Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.).
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