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Regulation of exon definition and apoptosis by the Ewing's Sarcoma Protein

ABSTRACT: The Ewing's Sarcoma Protein EWS belongs to the TET family (FUS/TLS, EWS, TAF15) of RNA and DNA binding proteins, implicated in DNA transcription, pre-mRNA splicing and maintenance of genome integrity. To identify in vivo RNA targets of EWS we performed a combinatorial approach of CLIP-Seq In this dataset, we include the expression data obtained from three biological replicates of HeLa cells transfected with either scrambled or siEWS oligonucleotides. These data allowed us to identify 805 genes affected at the expression level by EWS knockdown, of which 395 upregulated and 410 downregulated. Moreover, HJAY identified 206 differentially regulated alternative splicing events in 114 genes. Three biological replicates were labeled and hybridized onto Affymetrix HJAY

ORGANISM(S): Homo sapiens

SUBMITTER: Maria Paola Paronetto

PROVIDER: E-GEOD-47790 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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EWS siRNA knock-down in HeLa cell line

Project description:HeLa cell line was trasfected by a EWS siRNA oligo causing knock-down of EWS or a siRNA scrambled oligo Three biological replicates were labeled in direct and dye-swap microarray experiments and hybridized onto an Agilent custom splicing-sensitive microarray platform.

2011-09-19 | E-GEOD-22929 | biostudies-arrayexpress

shRNA mediated knockdown of TRA2B and SRSF3 in HEK293 cell line

Project description:We have independently knocked down TRA2B and SRSF3 in HEK293 cells to identify the sum of alternative splicing changes that results from depletion of each factor. Each was compared to a control transfection of the hairpin vector alone. In this set, 9 total samples were analyzed. There were three biological replicates for each of three conditions: knockdown control, TRA2B knockdown and SRSF3 knockdown. Arrays were analyzed for gene expression using GeneBase and for alternative splicing using MADS+ and OmniViewer software.

2012-04-30 | E-GEOD-36069 | biostudies-arrayexpress

Digitoxin treatment versus control in HEK293 cells

Project description:We treated HEK293 cells with the cardiotonic steroid digitoxin to identify alternative splicing changes as compared to DMSO treatment alone. In this set, 6 total samples were analyzed. There were three biological replicates for each of two conditions: DMSO treatment and Digitoxin treatment. Arrays were analyzed for gene expression using GeneBase and for alternative splicing using MADS+ and OmniViewer software.

2012-04-30 | E-GEOD-36058 | biostudies-arrayexpress

TDP-43 can directly affect splicing profiles and isoform production of genes involved in the apoptotic and mitotic cellular pathways

Project description:In recent times, high throughput screening analyses have broadly defined the RNA cellular targets of TDP-43, a nuclear factor involved in neurodegeneration. A common outcome of all these studies is that changing the expression levels of this protein can alter the expression of several hundred RNAs within cells. What still remains to be clarified is which changes represent direct cellular targets of TDP-43 or just secondary variations due to the general role played by this protein in RNA metabolism. Using a HTS-based splicing junction analysis we have now identified 162 splicing events that are consistent with being directly controlled by TDP-43. Validation of the data, both in neuronal and non-neuronal cell lines demonstrated that TDP-43 substantially alters the levels of isoform expression in four genes potentially important for neuropathology: MADD/IG20, STAG2, FNIP1, and BRD8. Most importantly, for MADD/IG20 and STAG2 these changes could also be confirmed at the protein level. These alterations were also observed in a cellular model that successfully mimics TDP-43 loss of function effects following its aggregation. These novel splicing events may represent potential biomarkers to predict disease onset, progression, and to test the efficacy of novel therapeutic agents to recover TDP-43 functional properties. We have performed an HTS-based splicing junction analysis of a series of stable cell lines that lack TDP-43, overexpress this factor, or express an RNA-binding mutant, in order to find splicing events, potentially associated with neurodegenerativce diseases, regulated by this splicing factor. Samples were analyzed in triplicate from: The following samples were analyzed in triplicate: wild-type HEK-293 cells, siTDP43-treated HEK-293 cells, siTDP43-treated HEK-293 cells overexpressing a flagged-wildtype TDP-43, siTDP43-treated HEK-293 cells overexpressing a RNA-binding deficient mutant.

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Regulation of FAS Exon Definition and Apoptosis by the Ewing Sarcoma Protein

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2014-05-21 | E-GEOD-48065 | biostudies-arrayexpress

RNA immunoprecipitation (RIP)-Chip analysis for EWS-bound mRNA

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2012-01-16 | E-GEOD-29313 | biostudies-arrayexpress

Regulation of exon definition and apoptosis by the Ewing's Sarcoma Protein

Project description:The Ewing's Sarcoma Protein EWS belongs to the TET family (FUS/TLS, EWS, TAF15) of RNA and DNA binding proteins, implicated in DNA transcription, pre-mRNA splicing and maintenance of genome integrity. To identify in vivo RNA targets of EWS we performed a combinatorial approach of CLIP-Seq In this dataset, we include the expression data obtained from three biological replicates of HeLa cells transfected with either scrambled or siEWS oligonucleotides. These data allowed us to identify 805 genes affected at the expression level by EWS knockdown, of which 395 upregulated and 410 downregulated. Moreover, HJAY identified 206 differentially regulated alternative splicing events in 114 genes.

2014-01-01 | GSE47790 | GEO

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2010-09-01 | E-GEOD-23522 | biostudies-arrayexpress

Regulation of NUMB alternative splicing by RBM5, RBM6 and RBM10 controls cancer cell proliferation

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2013-12-20 | E-GEOD-47431 | biostudies-arrayexpress

EMT inducers catalyze malignant transformation of mammary epithelial cells and drive tumorigenesis towards claudin-low tumors [human]

Project description:The newly identified claudin-low subtype of cancer is believed to represent the most primitive breast malignancies, having arisen from transformation of an early epithelial precursor with inherent stemness properties and metaplastic features. Challenging this hypothesis, we show both in vitro and in vivo that transcription factors inducing epithelial-mesenchymal transition can drive the development of claudin-low tumors from differentiated mammary epithelial cells, by playing a dual role in cell transformation and dedifferentiation. Human mammary epithelial cells (HMEC) were sequentially immortalized by hTert (HMEC-hTert), transduced with Twist1 or Zeb2 or Zeb1 and then with H-RasG12V. The gene expression profiles of the resulting HMEC-hTert-Twist1+Ras, HMEC-hTert-Zeb1+Ras and HMEC-hTert-Zeb2+Ras cell lines were defined. HMEC-hTert-Twist1+Ras and HMEC-hTert-Zeb2+Ras cell lines were additionally cultured in presence of TGFM-CM-^C? and their gene expression profiles were determined. The parental HMEC-hTert, the luminal MCF7 and the basal B MDMB157cell lines were used as controls.

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