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Expression data from embryonic stem cells following siRNA transfection of UPS members [Differentiation_ES]

ABSTRACT: While transcriptional regulation of stem cell self-renewal and differentiation has been extensively studied, only a small number of studies have addressed the roles for post-translational modifications in these processes. A key mechanism of post-translational modification is ubiquitination by the ubiquitin-proteasome system (UPS). Using UPS-targeted RNAi screens, we identify novel regulators of pluripotency and differentiation. We focus on two of these proteins, the deubiquitinating enzyme, Psmd14, and the E3 ligase, Fbxw7, and characterize their importance in ES cell pluripotency and cellular reprogramming.

ORGANISM(S): Mus musculus

PROVIDER: GSE39770 | GEO | 2012/08/01

SECONDARY ACCESSION(S): PRJNA171698

REPOSITORIES: GEO

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Expression data from embryonic stem cells following siRNA transfection of UPS members [self_renewal]

Project description:While transcriptional regulation of stem cell self-renewal and differentiation has been extensively studied, only a small number of studies have addressed the roles for post-translational modifications in these processes. A key mechanism of post-translational modification is ubiquitination by the ubiquitin-proteasome system (UPS). Using UPS-targeted RNAi screens, we identify novel regulators of pluripotency and differentiation. We focus on two of these proteins, the deubiquitinating enzyme, Psmd14, and the E3 ligase, Fbxw7, and characterize their importance in ES cell pluripotency and cellular reprogramming.

2012-08-01 | GSE39771 | GEO

Expression data from embryonic stem cells following siRNA transfection of UPS members [self_renewal]

2012-07-31 | E-GEOD-39771 | biostudies-arrayexpress

Expression data from embryonic stem cells following siRNA transfection of UPS members [Differentiation_ES]

2012-07-31 | E-GEOD-39770 | biostudies-arrayexpress

Expression data from embryonic stem cells following siRNA transfection of UPS members

Project description:This SuperSeries is composed of the following subset Series: GSE39770: Expression data from embryonic stem cells following siRNA transfection of UPS members [Differentiation_ES] GSE39771: Expression data from embryonic stem cells following siRNA transfection of UPS members [self_renewal] Refer to individual Series

2012-07-31 | E-GEOD-39772 | biostudies-arrayexpress

RNA-seq analysis between mouse UPS tumors (KP) and mouse UPS tumors without HIF-2alpha (KPH2)

Project description:Purpose: determine RNA expression differences in an unbiased fashion between UPS tumors derived from LSL-KrasG12D;Trp53-/- (KP) mice, and UPS tumors derived from LSL-KrasG12D;Trp53-/-;Epas1-/- (KPH2) mice. Epas1 encodes HIF-2alpha protein.

2015-12-31 | GSE67672 | GEO

RNA-seq analysis between mouse UPS tumors (KP) and mouse UPS tumors without HIF-2alpha (KPH2)

2015-12-31 | E-GEOD-67672 | biostudies-arrayexpress

Gene expression signature from tumor initiating population predicts clinical outcome in undifferentiated pleomorphic sarcoma (UPS)

Project description:Undifferentiated pleomorphic sarcomas (UPS) are thought to harbor a small population of cells with unique capability of tumor initiation and maintenance. These tumor initiating cells (TICs) are regarded as the drivers of cancer progression. However, the evidence for this tumor initiating cell (TIC) concept is based on the xenotransplantation assays in mice and the clinical relevance of the TIC concept remains unclear in UPS. We hypothesized that the distinct properties of the TICs would be reflected in the clinical outcome if the TIC concept is relevant in UPS. Here we performed global gene expression profiling of TIC-enriched side population (SP) fractions and non-SP fractions sorted from 15 UPS primary samples. Ninety-three genes were differentially expressed in between SP fractions and non-SP fractions. The UPS TIC gene expression signature score summarizing expression of these genes was calculated for a gene expression data and was correlated with clinical outcome. In the 15 samples used to generate the signature, patients with high scores in the SP fractions were associated with worse survival. We then tested the two independent published datasets with gene expression data on bulk unsorted samples, assuming that the TIC gene expression would persist in the non-TICs. Patients with high scores had significantly worse metastasis-free survival in both datasets. The significance of the score remained significant even considering for the known prognostic factor of UPS. Thus, gene expression signature derived from UPS TICs predicts clinical outcome, suggesting the clinical relevance of the TIC concept in UPS.

2016-02-01 | GSE55973 | GEO

Project description:FBXW7 modulates stress response by post-translational modification of HSF1

| PRJNA246390 | ENA

Genome-wide characterization of HSF1 binding in human WT and FBXW7 KO colon cancer cells under basal conditions and upon heat shock

Project description:FBXW7 modulates stress response by post-translational modification of HSF1 HSF1 orchestrates the heat-shock response upon exposure to heat stress and activates a transcriptional program vital for cancer cells. In this study we assayed for genome-wide localization of HSF1 enrichment in the HCT116 FBXW7 KO colon cells and their wild type counterpart in untreated cells and upon heat shock. These results revealed that accumulation of nuclear HSF1 in FBXW7 KO cells results in rewiring of the HSF1 transcriptional program. Five million cells were used for the ChIP and precipitated using 5 micrograms of antibody (cell signaling, 4356) against human HSF1

2015-02-20 | E-GEOD-57398 | biostudies-arrayexpress

Genome-wide characterization of HSF1 binding in human WT and FBXW7 KO colon cancer cells under basal conditions and upon heat shock

2015-02-20 | GSE57398 | GEO

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