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Genome-wide analysis of REST knockdown responsive gene expression in mouse ES cells

ABSTRACT: Analysis of gene expression profiling upon REST shRNA knockdown in mouse ES cells for 72 hours,

ORGANISM(S): Mus musculus

PROVIDER: GSE28141 | GEO | 2011/04/01

SECONDARY ACCESSION(S): PRJNA143159

REPOSITORIES: GEO

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Genome-wide analysis of REST knockdown responsive gene expression in mouse ES cells

Project description:Analysis of gene expression profiling upon REST shRNA knockdown in mouse ES cells for 72 hours, Total RNA obtained from pSuper vector control and REST shRNA treatment for 72 hours using Invitrogen RNA extraction kit.

2011-04-01 | E-GEOD-28141 | biostudies-arrayexpress

REST ChIP-chip and knockdown expression profiling

Project description:This SuperSeries is composed of the following subset Series: GSE28141: Genome-wide analysis of REST knockdown responsive gene expression in mouse ES cells GSE28233: Genome-wide maps of REST and its cofactors in mouse E14 cells Refer to individual Series

2011-03-31 | E-GEOD-28289 | biostudies-arrayexpress

REST knockdown in LNCaP prostate cancer cells

Project description:LNCaP cells were transfected with 3 different REST siRNAs Transcriptomics analysis was performed to compare gene expression changes induced by REST knockdown

2013-10-22 | GSE51461 | GEO

REST knockdown in LNCaP prostate cancer cells

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2013-10-22 | E-GEOD-51461 | biostudies-arrayexpress

The role of Rif1 in ES cells

Project description:Purpose:The goals of this study are to understand the mechanisms underlying reduced self-renewal and loss of pluripotency by depletion of Rif1. Methods: We performed global gene expression analysis of Rif1 knockdown ES cell lines using Affymetrix 430 2.0 arrays, compared to shRNA controls. J1 ES cells were transfected with Control shRNA and Rif1 shRNA using lipofectamine 2000. Forty-eight hours after transfection, cells were collected for global gene expression analysis using Affymetrix mouse genome 430 2.0 array. Stable F1 Rif1 knockdown ES cells at passage 16 were used for long-term gene expression chip microarray using Affymetrix mouse genome 430 2.0 array.

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ChIP-Seq data for REST, MCAF1, Ring1b and H4K20me3 in mouse embryonic stem (ES) cells

2011-01-19 | GSE26680 | GEO

ChIP-Seq data for REST, MCAF1, Ring1b and H4K20me3 in mouse embryonic stem (ES) cells

Project description:Multiple protein complexes and histone marks have been implicated and/or associated with gene repression in ES cells. To gain insights into repressive complexes present at repressed genes and their associated chromatin state, we profiled REST, MCAF1, Ring1b and H4K20me3 in mouse ES cells. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against REST, MCAF1, Ring1b and H4K20me3.

2011-01-19 | E-GEOD-26680 | biostudies-arrayexpress

CDK8 and MED12 knockdown in R1 mouse ES cells

Project description:Transcriptional profiling of R1 mouse ES cells infected with non-targeting control (NTC) shRNA and two different shRNA sequences against Cdk8 (shCdk8-1 and shCdk-2) and Med12 (shMed12-1 and shMed12-2).

2012-03-05 | GSE30816 | GEO

PCSK9 knockdown in EndoC-bH1 cells at 72 hours

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Effect of Tet1-knockdown on gene expression in mouse ES cells cultured in ES and TS cell culture conditions

Project description:TET-family enzymes convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in DNA. Tet1 and Tet2 are Oct4-regulated enzymes that together sustain 5hmC in mouse embryonic stem (ES) cells. ES cells depleted of Tet1 by RNAi show diminished expression of the Nodal antagonist Lefty1, and display hyperactive Nodal signalling and skewed differentiation into the endoderm-mesoderm lineage in embryoid bodies in vitro. In Fgf4- and heparin-supplemented culture conditions that favor derivation of trophoblast stem (TS) cells, Tet1-depleted ES cells activate the trophoblast stem cell lineage determinant Elf5 and can colonize the placenta in mid-gestation embryo chimeras. Consistent with these findings, Tet1-depleted ES cells form aggressive hemorrhagic teratomas with increased endoderm, reduced neuroectoderm and ectopic appearance of trophoblastic giant cells. Thus Tet1 functions to regulate the lineage differentiation potential of ES cells. Here, we performed whole-genome transcriptome profiling of ES cells stably depleted of Tet1 by shRNA knockdown (Tet1-kd) cultured in either standard ES cell or in TS cell culture conditions. Gene expression changes in Tet1-kd ES cells were fairly modest compared to control (GFP-kd) cells, although gene ontology (GO) analysis of differentially expressed genes yielded many terms related to embryonic development and cell cycle regulation. In TS cell culture conditions, a core set of genes defining trophectodermal cell differentiation, including Cdx2, Eomes and Tead4, was enriched in Tet1-kd compared to GFP-kd cells.

2011-02-07 | GSE26900 | GEO

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