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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Harold Moses

PROVIDER: E-GEOD-54756 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transforming growth factor beta receptor type III is a tumor promoter in mesenchymal-stem like triple negative breast cancer.

Jovanović Bojana B Beeler J Scott JS Pickup Michael W MW Chytil Anna A Gorska Agnieszka E AE Ashby William J WJ Lehmann Brian D BD Zijlstra Andries A Pietenpol Jennifer A JA Moses Harold L HL

Breast cancer research : BCR 20140701 4

<h4>Introduction</h4>There is a major need to better understand the molecular basis of triple negative breast cancer (TNBC) in order to develop effective therapeutic strategies. Using gene expression data from 587 TNBC patients we previously identified six subtypes of the disease, among which a mesenchymal-stem like (MSL) subtype. The MSL subtype has significantly higher expression of the transforming growth factor beta (TGF-β) pathway-associated genes relative to other subtypes, including the T ...[more]

PMID: 24985072

Similar Datasets

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.

2014-02-06 | GSE54756 | GEO

Gene expression profiling of transmitochondrial cybrids (triple negative breast cancer cells in SUM159 background)

Project description:We used a transmitochondrial cybrid (cybrids)-based discovery approach to identify mitochondria-regulated cancer pathways in TN BCa. Cybrids were generated under a moderately metastatic TN BCa cell line SUM159 as the common nuclear background with mitochondria from benign breast epithelium (A1N4) and moderately metastatic (SUM159) TN BCa cells. In vitro and in vivo studies suggested that even under the common moderately cancerous nuclear background, mitochondria from benign cells inhibit and metastatic cell induce cancer properties of a moderately aggressive TN BCa cell. Gene expression studies identified c-Src onco-pathway as one of the major cancer pathways altered according to the mitochondria status of the cybrids. SUM159 Ï0 cells were used as nuclear donor and A1N4 and SUM 159 cells were used as mitochondrial donor cells. The two groups were profiled for gene expression using microarrays. two group comparison (159/SUM159 vs A1/SUM159)

2016-04-14 | E-GEOD-72319 | biostudies-arrayexpress

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 OA gene expression profiling was performed with Affymetrix Human Gene 1.1 st array was performed in and independent cohort of 23 OA patients

2013-04-01 | E-GEOD-43191 | biostudies-arrayexpress

Human TNBC Cells 72h Treatment with 4.5nM OTSSP167 MELK Inhibitor vs. DMSO Control (SUM159)

Project description:Microarray comparing TNBC cells treated for 72 hours with OTSSP167 MELK Inhibitor and control (DMSO) Two-condition arrays: SUM159 cells were treated with either 4.5nM OTSSP167 MELK Inhibitor or 0.045% DMSO for 72h. Two biological replicates, one per array, with a dye swap (technical replicate).

2017-05-01 | E-GEOD-71026 | biostudies-arrayexpress

Human TNBC Cells 72h Treatment with 45nM OTSSP167 MELK Inhibitor vs. DMSO Control (SUM159)

Project description:Microarray comparing TNBC cells treated for 72 hours with OTSSP167 MELK Inhibitor and control (DMSO) Two-condition arrays: SUM159 cells were treated with either 45nM OTSSP167 MELK Inhibitor or 0.045% DMSO for 72h. Two biological replicates, one per array, with a dye swap (technical replicate).

2017-05-01 | E-GEOD-71027 | biostudies-arrayexpress

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.

2012-06-24 | E-GEOD-38906 | biostudies-arrayexpress

RNA interference uncouples the function of a long noncoding RNA product from that of its transcription [SUM159]

Project description:Long noncoding RNAs (lncRNAs) regulate gene expression via their RNA product or through transcriptional interference, yet a strategy to differentiate these two processes is missing. We employed siRNAs to specifically target GNG12-AS1, a lncRNA overlapping the tumour suppressor DIRAS3, transcriptionally or post-transcriptionally. lncRNA transcriptional silencing by siRNA was mediated by Argounate 2 and led to the upregulation of DIRAS3 transcription through switch in RNA polymerase II binding and active histone marks. Conversely, post-transcriptional silencing of GNG12-AS1 had no effect on DIRAS3 expression. Thus, our findings reveal how RNAi machinery can be used to decouple the process and products of lncRNA transcription. The goal of this study was to identify genes regulated by long noncoding RNA GNG12-AS1 in human cells RNA was extracted from human cells (HB2, SUM159) treated with control and GNG12-AS1 siRNAs. The analysis was performed with six biological replicates for each cell line.

2015-11-12 | E-GEOD-60561 | biostudies-arrayexpress

Expression data to identify putative transcriptional targets of ZNF165 in Triple Negative Breast Cancer (TNBC)

Project description:We found that the cancer testis antigen, ZNF165, is required for viability and can modulate TGFÎ²-induced gene expression in mesenchymal, Claudin-Low, TNBC. We employed the Affymetrix microarray platform to uncover transcriptionally modulated genes following ZNF165 depletion and TGFÎ² stimulation using the Claudin-low TNBC tumor-derived cell lines, SUM159 as a model. Our results provide insight into how ZNF165 globally modulates TGFÎ² signaling. We used microarray analysis to uncover the transcriptional network controlled by ZNF165 and clarify the role of ZNF165 in global TGFÎ² signaling SUM159 and WHIM12 cells were reverse transfected with either non-targeting or ZNF165 siRNA. For SUM159 cells, sixty hours post-transfection, cells were exposed to TGFÎ² for 3 hours. For WHIM12, forty eight hours post-transfection, cells were exposed to TGFÎ² for 3 hours. Total RNA was isolated and hybridized on to Affymetrix microarrays. Each experiment was repeated three times.

2015-11-09 | E-GEOD-63984 | biostudies-arrayexpress

Gene expression of SUM159-mir100 ALDH+ and ALDH- cells from CTRL or mir100-overexpressing group

Project description:Emerging evidence suggest that miRNAs play an essential role in self-renewal and differentiation of normal and malignant stem cells by regulating the expression of key stem cell regulatory genes. Here we demonstrate that mir-100 expression is related to cellular differentiation state with lowest expression in cells displaying stem cell markers. Utilizing a tetracycline inducible lentivirus driving mir-100 expression, we found that mir-100 overexpression decreased breast cancer stem cells (BCSCs) and inhibited cancer cell proliferation in vitro and in mouse xenografts by targeting SMARCA5, SMARCD1 and BMPR2. In order to determine the cellular targets of mir-100 in BCSCs and non-BCSCs, ALDH-positive and -negative populations of pTRIPZ-SUM159-mir-100 cells were separated and cultured in suspension for ten hours in the presence or absence of DOX. Gene expression profiles of the four populations were determined utilizing Affymetrix microarrays

2014-12-04 | E-GEOD-59361 | 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

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