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E-MEXP-2088

ABSTRACT: Transcription profiling by array of mouse embryonic stem cells after induction of doxycycline-inducible Xist transgene on chromosome 12

PROVIDER: E-MEXP-2088 | ExpressionAtlas | 2014-07-03

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MEXP-2088-analysis-methods.tsv	Tabular
	E-MEXP-2088-atlasExperimentSummary.Rdata	Rdata
	E-MEXP-2088-configuration.xml	Xml
	E-MEXP-2088-percentile-ranks.tsv	Tabular
	E-MEXP-2088.condensed-sdrf.tsv	Tabular

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Transcription profiling of mouse embyronic stem cells expressing the doxycycline-inducible Xist cDNA transgene inserted into chromosome 12 to study of Xist RNA mediated silencing

Project description:A doxycycline-inducible Xist cDNA transgene was introduced into mouse chromosome 12 at approximately 110Mb (NCBI build m36). Insertion of the transgene was heterozygous, so only one copy of chromosome 12 carried the transgene, and the other chromosome 12 was wild-type. Upon doxycycline induction, the transgene is expressed, producing Xist transgene RNA which localises to autosomal material in cis, leading to silencing of genes adjacent to the transgene. Due to the heterozygous nature of transgene insertion and the cis nature of silencing, for any silenced gene, the maximum possible downregulation in expression levels was 50%. To quantify the changes in the levels of gene expression in response to Xist transgene expression, total RNA was extracted from differentiated ES cells treated with doxycycline. As background control, total RNA was also prepared from uninduced, differentiated ES cells (cultured in parallel to doxycycline-treated cells). The total RNA was then used to make labelled cRNA, which was hybridised to an Affymetrix GeneChip Mouse Genome 430 2.0 array.

2010-05-10 | E-MEXP-2088 | biostudies-arrayexpress

Transcription profiling of mouse embryonic stem cells with a doxycycline-inducible Xist cDNA transgene introduced into chromosome 17

Project description:A doxycycline-inducible Xist cDNA transgene was introduced into mouse chromosome 17 at approximately 71.24Mb (NCBI Build m36). Insertion of the transgene was heterozygous, so only one copy of chromosome 17 carried the transgene, and the other chromosome 17 was wild-type. Upon doxycycline induction, the transgene is expressed, producing Xist transgene RNA which localises to autosomal material in cis, leading to silencing of genes adjacent to the transgene. Due to the heterozygous nature of transgene insertion and the cis nature of silencing, for any silenced gene, the maximum possible downregulation in expression levels was 50%. To quantify the changes in the levels of gene expression in response to Xist transgene expression, total RNA was extracted from undifferentiated and differentiated ES cells treated with doxycycline. As background control, total RNA was also prepared from uninduced cells (both undifferentiated and differentiated, cultured in parallel to doxycycline-treated cells). The total RNA was then used to make labelled cRNA, which was hybridised to an Affymetrix GeneChip Mouse Genome 430 2.0 array.

2010-05-10 | E-MEXP-2087 | biostudies-arrayexpress

E-MEXP-1862

Project description:Transcription profiling by array of mouse embryonic stem cells infected with Salmonella typhimurium

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Transcription profiling of mouse embryonic stem cells with a doxycycline-inducible Xist cDNA transgene introduced into chromosome 3

Project description:A doxycycline-inducible Xist cDNA transgene was introduced into mouse chromosome 3 at approximately 99.79Mb (NCBI Build m36). Insertion of the transgene was homozygous, so only one copy of chromosome 3 carried the transgene, and the other chromosome 3 was wild-type. Upon doxycycline induction, the transgene is expressed, producing Xist transgene RNA which localises to autosomal material in cis, leading to silencing of genes adjacent to the transgene. Due to the homozygous nature of transgene insertion and the cis nature of silencing, for any silenced gene, the maximum possible downregulation in expression levels was 50%. To quantify the changes in the levels of gene expression in response to Xist transgene expression, total RNA was extracted from undifferentiated and differentiated ES cells treated with doxycycline for three days. As background control, total RNA was also extracted from uninduced cells (both undifferentiated and differentiated, cultured in parallel to doxycycline-treated cells). cRNA was labelled from the total RNAs, and then hybridised to Affymetrix GeneChip Mouse Genome 430 2.0 arrays.

2010-05-10 | E-MEXP-2086 | biostudies-arrayexpress

RBM15 CoIP in mouse Embryonic Stem cells

Project description:RBM15 interactome has been determined in mouse Embryonic Stem cells. The cells express inducible emGFP-PreScission-RBM15 alongside with inducible Xist RNA.

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E-MTAB-6806

Project description:Transcription profiling by RNA-seq during NuRD complex induction in mouse embryonic stem cells

2018-06-04 | E-MTAB-6806 | ExpressionAtlas

E-TABM-673

Project description:Transcription profiling by array of mouse embryonic stem cells cultured with LY294002

2014-07-03 | E-TABM-673 | ExpressionAtlas

Impact of flanking chromosomal sequences on localization and silencing by the ncRNA XIST

Project description:We performed RNA-seq and ChIP-seq on clones of human cell lines carrying an inducible XIST transgene on 1p, 8p, or 12q to study the effects of allelic silencing in cis Total gene expression and allelic changes were examined in HT1080 clones carrying an inducible XIST transgene on 1p, 8p, or 12q after induction by doxycycline. A replicate was done for the 8p clone treated with DOX. An additional 1p clone integrated with an empty vector, and an 1p, 8p, and 12q clone without induction were included as controls. ChIP was performed on the 8p clone to investigate the changes in H3K27 acetylation and trimethylation.

2015-09-02 | E-GEOD-68109 | biostudies-arrayexpress

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Project description:Transcription profiling by array of mouse embryonic stem cells after treatment with cisplatin

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Gene Expression Analysis of Sox17-induced Mouse Embryonic Stem Cells

Project description:To determine the effect of Sox17 overexpression in mouse embryonic stem (ES) cells, we performed gain-of-function analysis by generating ES cell lines carrying a doxycycline inducible FLAG-tagged Sox17 transgene. We treated Sox17-inducible ES cells with doxycycline, collected RNA and performed genome-wide transcriptional analysis. We found that genes invovled in adhesion function and basement membrane establishment were transcriptionally upregulated in ES cells upon induction of Sox17. We also observed downregulation in the transcription of genes involved in pathways known to be functionally important for ES cell pluripotency and self-renewal. However, Sox17 expression was not sufficient to rapidly down-regulate Sox2, Nanog, and Oct4. Two independent doxycycline inducible Sox17-overexpressing mouse embryonic stem cells were derived. The genes expression changes in the Sox17-induced cells were compared to untreated (no doxycycline) controls and to control cells treated with or without doxycycline. The total RNA from these samples were amplified using Ambion Illumina TotalPrep RNA Amplification kit and arrayed on Illumina MouseRef8 v2 chips.

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