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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: gene expression

ABSTRACT: 10 Breast cancer cell lines profiled on the Affymetrix U133 Plus 2.0 platform used in conjunction with matched DNA copy number and DNA methylation data for integrative analysis. In total, 10 samples were used. The MCF10A profile used as normal was obtained from GSM254525 and the remaining 2 cell lines were obtained from caBIG. Full RMA normalized expression profile is attached.

ORGANISM(S): Homo sapiens

SUBMITTER: Raj Chari

PROVIDER: E-GEOD-17768 | 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.

Chari Raj R Coe Bradley P BP Vucic Emily A EA Lockwood William W WW Lam Wan L WL

BMC systems biology 20100517

<h4>Background</h4>Genomics has substantially changed our approach to cancer research. Gene expression profiling, for example, has been utilized to delineate subtypes of cancer, and facilitated derivation of predictive and prognostic signatures. The emergence of technologies for the high resolution and genome-wide description of genetic and epigenetic features has enabled the identification of a multitude of causal DNA events in tumors. This has afforded the potential for large scale integration ...[more]

PMID: 20478067

Similar Datasets

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

Project description: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

2010-12-31 | E-GEOD-21541 | biostudies-arrayexpress

Gene Expression in MCF10A cells through Differentiation on Transwells

Project description:To further understand the differences occurring in MCF10A cells as they polarize and differentiate in the TranswellÂ® model, we performed gene expression profiling with Affymetrix Human Genome U133 Plus 2.0 Arrays. Four experimental time points, were sampled: conventional cultures of MCF10A cells grown on plastic (Monolayer) and MCF10A cells plated on TranswellsÂ® sampled at three TEER values, 200-300 Î© cm2 (Base), 1400-1600 Î© cm2 (Midpoint), and 3000-3200 Î© cm2 (Plateau). Experiment Overall Design: Cells are grown in monolayer to 90-95% confluency, trypsinized and counted for seeding onto permeable supports (TranswellÂ®, 0.4 Âµm pores, polyester) in normal growth medium. MCF10A cells are seeded on 12-well TranswellsÂ® (Corning) at 105 cells/cm2. Both chambers of media were changed strictly on a 24-hour schedule. Transepithelial electrical resistance (TEER) is measured daily with Epithelial Volt-Ohm Meter (EVOM; World Precision Instruments), prior to media change. Total RNA was isolated at the indicated TEER listed above. Canonical monolayer MCF10A cells served as a control comparison. Each time point was performed on triplicate arrays except for Plateau (n=4).

2008-06-11 | E-GEOD-10070 | biostudies-arrayexpress

Mouse_embryoid Body_Retinoic acid treatment

Project description:S6K1 Knockout mice has a lean phenotype and resitant to a High Fat Diet-induced obesity (Um S.H., Nature, 2004). Adipocyte differentiation consists of two step, first, commitment from stem cell to adipocyte progenitors and second, terminal differentiation from adipocyte progenitors to mature adipocyte. We studied S6K1-dependent gene expression regulation in early stage of commitment by employing ES cell(ESC)-Embryoid Bodies(EBs) differentiation model. We established stable ES cell lines infected with either control non-silencing shRNA (shNS) or S6K1 targetting shRNA (shS6K1). Each sample was treated with retinoic acid for 3 days to induce adipogenesis, then gene expression profile was analyzed employing microarrays and up-regulated and down-regulated genes were selected for analysis. Mouse Embryoid Bodies (approximately 1000 EBs per sample) were treated with retinoic acid (1ÂµM) for 3 days then collected for RNA extraction and hybridization on Affimetrix microarray. Two biological replicates were each performed for EBs prepared from either shNS ESCs or shS6K1 ESCs.

2010-05-14 | E-GEOD-20349 | biostudies-arrayexpress

YAP conveys an invasive phenotype to clear cell renal cell carcinoma cell lines via endothelin-2

Project description:To determine the biological mechanisms underlying the oncogenic properties of YAP in ccRCC the human ccRCC cell line MZ1774 was transduced with lentivirus containing a shRNA-cassette targeting YAP-mRNA. Expression profiles of MZ1774 YAP knockdown cells were compared to mock-transduced control cells. Total RNA from MZ1774 cells stably expressing shRNA directed against YAP compared to mock-transduced MZ1174 cells

2014-12-23 | E-GEOD-50053 | biostudies-arrayexpress

Estrogen-driven Prolactin-mediated Gene Expression Networks Hormone Induced Prostatic Dysplasia

Project description:Emerging evidence suggests that estrogen and prolactin (PRL) play a key role in prostate cancer development, yet their relationship and molecular actions in prostate is not well understood. To address this issue, we made the first direct comparison of estrogen and PRL actions in the Noble rat (NBL) prostate dysplasia model. Prostatic dysplasia in lateral prostate (DLP) has been induced by elevated circulating levels of estrogen and PRL in NBL with estrogen (E2)-filled implants, while physiological level of testosterone (T) was maintained with T-filled implants. The effect of estrogen and PRL was studied by using ICI and bromocriptine (Br) as their respective blockers, both can effectively inhibited dysplasia development under T+E2 induction. Transcript expression profile of the four treatment groups (Control, T+E2, T+E2+Br, and T+E2+ICI) has been characterized in this array.

2010-05-09 | E-GEOD-17819 | biostudies-arrayexpress

Gene expression profiling of skeletal myoblast differentiation and exposure to TNF-alpha or IGF1

Project description:Skeletal myocyte differentiation involves fusion of myoblasts to multinucleated myotubes. In vitro differentiation can be induced by serum withdrawal. The differentiation process is negatively regulated by pathological concentrations of TNF-alpha but can be positively regulated by IGF1. This study focuses on elucidating the expression kinetics of mRNAs right after induction of differentiation (4 hours), during very early differentiation (12 h), early differentiation (24 h) as well as later differentiation (72 h) and how gene expression is modulated by TNF-alpha or IGF1, respectively.

2015-04-05 | E-MTAB-3474 | biostudies-arrayexpress

Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system (BeadChip)

Project description:Gene regulatory elements such as enhancers have profound effects on cellular function, health, and disease. Our understanding of mammalian enhancer function is limited by the lack of a technology that would allow for a rapid and thorough test of their cell type-specific function. Here, we describe a novel Cas9-effector system that enables rapid testing and functional annotation of native enhancers in embryonic stem cells. Total RNA obtained from R26 dCas9-effector mESC lines after viral delivery of sgRNAs directed against proximal promoter or enhancer regions

2015-03-03 | E-GEOD-64057 | biostudies-arrayexpress

Expression data from NRK-52E cells treated with aristolochic acids for 6h, 24h and 72h

Project description:In this study we have examined the effect of sub-cytotoxic exposure to aristolochic acids (1.65µM) at 6h, 24h and 72h on the whole-genome expression profile in a rat proximal renal tubule cell line (NRK-52E). We used microarrays to detail the mechanism of toxicity and possibly carcinogenicity of aristolochic acids in rat renal proximal cells. NRK-52E cells were cultured to confluence on 6-well plates. Cells were then exposed to aristolochic acid dissolved in DMSO (0.1%) at the IC10 concentration at 72h (1.65 ?M) or DMSO only as control. After 6h, 24h and 72h the medium was removed and RNA was extracted from the cells. Three studies were conducted at each time point.

2015-07-02 | E-GEOD-68687 | biostudies-arrayexpress

Transcription profiling of human tongue carcinoma cells treated with emdogain and TGF beta1

Project description:Background: The composition of Emdogain® (EMD) is unclear, but it has been postulated to contain transforming growth factor-beta-1 (TGF-beta1) as the main functioning cytokine. The purpose of this study was to compare target genes of EMD and TGF-beta1 on invasive oral carcinoma HSC-3 cells. Particular focus was on matrix metalloproteinase (MMP) family genes. <br>Methodology/Principal Findings: Affymetrix microarrays were conducted to study differentially (P<0.05) expressed genes in HSC-3 cells after 6h and 24h of EMD (200 ?g/ml) or TGF-beta1 (10 ng/ml) incubations. Gene Ontology (GO) enrichment analyses from the regulated genes were also conducted. After 6h of EMD or TGF-?1 treatment, 48 and 393 genes, respectively, were regulated. After 24h incubations, only 12 genes by EMD but 346 genes by TGF-beta1 were regulated. Among the most regulated genes by both of the study reagents were several genes commonly regulated in carcinomas, including MMP-9 and -10. The expression of MMP-10 by EMD treated carcinoma cells was also verified in protein level. <br>Conclusions/Significance: Our results show that EMD and TGF-beta1 can regulate genes related to carcinogenesis, but TGF-beta1 regulates significantly greater number of genes. This suggests that TGF-beta1 cannot be present in EMD at the studied concentration, if present at all.<br>

2010-04-30 | E-MEXP-2645 | biostudies-arrayexpress

Comparisons between fully and partially reprogrammed iPS cells induced by pMX-Klf4, pMX-Oct4 and pMX-Sox2 retroviruses

Project description:Induced pluripotent stem (iPS) cell reprogramming is a gradual epigenetic process that reactivates the pluripotent transcriptional network by erasing and establishing heterochromatin marks. Here, we characterize the physical structure of heterochromatin domains in full and partial mouse iPS cells by correlative Electron Spectroscopic Imaging (ESI). In somatic and partial iPS cells, constitutive heterochromatin marked by H3K9me3 is highly compartmentalized into chromocenter structures of densely packed 10 nm chromatin fibers. In contrast, chromocenter boundaries are poorly defined in pluripotent ES and full iPS cells, and are characterized by unusually dispersed 10 nm heterochromatin fibers in high Nanog-expressing cells, including pluripotent cells of the mouse blastocyst prior to differentiation. This heterochromatin reorganization accompanies retroviral silencing during conversion of partial iPS cells by Mek/Gsk3 2i inhibitor treatment. Thus, constitutive heterochromatin reorganization serves as a novel biomarker with retroviral silencing for identifying iPS cells in the very late stages of reprogramming. We compared the expression profiles of partially and fully reprogrammed iPS cell lines derived from CD1 mouse embryonic fibroblasts (MEFSs) by retroviral reprogramming (pMX-Oct4, pMX-Klf4 and pMX-Sox2). to the differentiated MEFS and the J1 embryonic stem cell line. We also studied the effect of a 2i cocktail treatment in partially reprogrammed iPS cells.

2011-09-21 | E-GEOD-21595 | biostudies-arrayexpress

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