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Genome wide-DNA methylation analysis of articular chondrocytes reveals a cluster of osteoarthritic patients (gene expression)

ABSTRACT: The aim of this study is to identify, for the first time, the genome-wide DNA methylation profiles of human articular chondrocytes from OA and healtly cartilage samples. A subsequent validation of methylation profiles were performed in an idependent cohort of OA samples with Affymetrix Hugene 1.1 st array This represents the gene expression component of the study only OA gene expression profiling was performed with Affymetrix Human Gene 1.1 st array was performed in and independent cohort of 23 OA patients

ORGANISM(S): Homo sapiens

SUBMITTER: Juan Fernandez Tajes

PROVIDER: E-GEOD-43191 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide DNA methylation analysis of articular chondrocytes reveals a cluster of osteoarthritic patients.

Fernández-Tajes Juan J Soto-Hermida Angel A Vázquez-Mosquera Maria E ME Cortés-Pereira Estefania E Mosquera Alejandro A Fernández-Moreno Mercedes M Oreiro Natividad N Fernández-López Carlos C Fernández Jose Luis JL Rego-Pérez Ignacio I Blanco Francisco J FJ

Annals of the rheumatic diseases 20130316 4

<h4>Objective</h4>Alterations in DNA methylation patterns have been found to correlate with several diseases including osteoarthritis (OA). The aim of this study was to identify, for the first time, the genome-wide DNA methylation profiles of human articular chondrocytes from OA cartilage and healthy control cartilage samples.<h4>Methods</h4>DNA methylation profiling was performed using Illumina Infinium HumanMethylation27 in 25 patients with OA and 20 healthy controls. Subsequent validation was ...[more]

PMID: 23505229

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Genome wide-DNA methylation analysis of articular chondrocytes reveals a cluster of osteoarthritic patients (gene expression)

Project description:The aim of this study is to identify, for the first time, the genome-wide DNA methylation profiles of human articular chondrocytes from OA and healtly cartilage samples. A subsequent validation of methylation profiles were performed in an idependent cohort of OA samples with Affymetrix Hugene 1.1 st array This represents the gene expression component of the study only

2013-04-01 | GSE43191 | GEO

Expression data from TGFBR3 controls and TGFBR3 knockdown of SUM159 3D cultures

Project description:The objective of this experiment was to determine global gene expression change in triple negative cell line upon knockdown of TGFBR3. Genotype specific differences in expression profiles have been evaluated using human HuGene1.0-ST affymetrix array. RNA was extracted from SUM159 controls and SUM159 TGFBR3KD cells cultured in 3-dimensional in vitro system. Control (N=3) and TGFBR3KD (N=3) samples were hybridized to the Human gene 1.0 ST array, scanned with Affymetrix using AGCC v. 3.2.4 and then analyzed in R 3.0.1 using the oligo package.

2014-02-06 | E-GEOD-54756 | biostudies-arrayexpress

Expression data from human peripheral blood lymphocytes stimulated with anti-CD3 and anti-CD28 antibodies.

Project description:Peripheral blood lymphocytes were separated in the Ficoll gradient and subjected for stimulation with anti-CD3 and anti-CD28 antiobodies upon time (6h, 12h and 18h). Next, total RNA was isolated and trenscriptional analysis of stimulated cells was performed. 11 total samples were analysed. Analysis was performed using samples from two healthy donors and one sample from patient. Unstimulated samples were used as a controls.

2013-02-25 | E-GEOD-29624 | biostudies-arrayexpress

Gene expression data from 1833 cells and 1833 cells depleted of BACH1 mRNA expression

Project description:The transcription factor BACH1 is a master regulator of human breast cancer metastasis. Here we use gene expression array analysis to identify and compare the genes regulated by BACH1 depletion in a metastatic human breast cancer cell line. Total RNAs were extracted from vector control 1833 cells or 1833 cells with shBACH mRNA BACH1 depletion. Affymetrix GeneChip Human Gene 1.0 ST Arrays were performed to detail the gene expression and identify the genes regulated by BACH1in metastatic human breast cancer cells.

2013-10-31 | E-GEOD-50226 | biostudies-arrayexpress

Comparison of peripheral blood leucocyte subsets in healthy individuals

Project description:CD4+ T cells, CD8+ T cells, CD14+ monocytes, and CD16+ neutrophils from the peripheral blood of 5 healthy individuals were isolated and their ex vivo transcriptomic profiles measured.

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Characterisation of Anaplastic Large Cell Lymphoma Stem Cells

Project description:Anaplastic Large Cell Lymphoma (ALCL) is propagated by cancer stem cells which are identified by their ability to efflux dye and hence reside in the side population (SP) on FACS analysis. In order to understand the origins of these ALCL SP cells we purified SP and main population (MP; SP-depleted) cell from the ALCL cell line SUDHL-1. On comparison of the gene expression signatures derived from these 2 cellular populations distinct branches dividing the SP and MP populations present indicating that they are distinct subsets within the bulk tumour. We sought to obtain pure populations of SP and MP cells from human SUDHL-1 Anaplastic Large Cell Lymphoma (ALCL) cell line. SUDHL-1 cells were stained with Hoechst 33342 dye, analysed using MoFlo Cell Sorter with UV lasers. The cells were then sorted in triplicates and subjected to RNA extraction. The extracted RNA was subjected to gene expression microarray using the Affymetrix Human Gene 1.0 ST Array.

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Genome wide-DNA methylation analysis of articular chondrocytes reveals a cluster of osteoarthritic patients (methylation)

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2013-04-01 | E-GEOD-43269 | biostudies-arrayexpress

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2011-12-20 | E-GEOD-34524 | biostudies-arrayexpress

BT474 tumors and MCF10A-HER2/3 cells in the presence or absence of SHP2

Project description:This SuperSeries is composed of the following subset Series: GSE34523: BT474 tumors in the presence or absence of SHP2 GSE34524: MCF10A-HER2/3 cells grown in 3D cultures in the presence or absence of SHP2 Refer to individual Series

2011-12-20 | E-GEOD-34525 | biostudies-arrayexpress

Primary TNBC tumor in the presence or absence of SHP2

Project description:The first bona fide PTP proto-oncogene was the Src-homology 2 domain-containing phosphatase SHP2 (encoded by PTPN11), an ubiquitously expressed PTP that transduces mitogenic, pro-survival, cell fate and/or pro-migratory signals from numerous growth factor-, cytokine- and extracellular matrix receptors. In malignancies, SHP2 is hyperactivated either downstream of oncoproteins or by mutations.We provide analysis of a primary triple-negative breast tumor grown as xenografts in the presence or absence of SHP2 for 30 days. A primary triple-negative breast tumor (BT8) was transduced with a doxycycline-inducible lentiviral vector expressing a CTRL miR or SHP2 miR1 or SHP2 miR2. Cells from each group were injected in immunodeficient mice and after tumor development, the knockdown of SHP2 was induced for 30 days in vivo. At day 30, tumors were dissected and RNA isolated for gene expression analysis.

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