Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA90633 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To examine the transcriptional changes that occur following alpha4 deletion, RNA microarray analysis was performed using RNA from alpha4-floxed MEFs 48 hours after infection with the Cre-containing or Vector control virus. Keywords: other
2004-09-01 | GSE1708 | GEO
Project description:To examine the transcriptional changes that occur following alpha4 deletion, RNA microarray analysis was performed using RNA from alpha4-floxed MEFs 48 hours after infection with the Cre-containing or Vector control virus.
2008-06-11 | E-GEOD-1708 | biostudies-arrayexpress
Project description:The purpose of the study was to determine what genes in DN2 pro-T cells are immediately regulated by the transcription factor GATA-3, either as activation targets or as repression targets. To do this, two pairs of Gata3-floxed and control pro-T cells were generated and analyzed by RNA-seq within the first day of deletion of the Gata3 gene. Pro-T cells were generated by differentiation in vitro on OP9-DL1 monolayers of fetal liver-derive precursors from wildtype or Gata3-floxed mice, and the Gata3 gene was acutely deleted by transduction with Cre retroviral vector. Within 20 hr after transduction, samples of acutely Gata3-deleted and control DN2 cells were sorted and RNA prepared for RNA-seq analysis. High-throughput sequencing of the samples was carried out. Experimental Gata3 deleted samples in both cases were Gata3-floxed, ROSA26R-EYFP samples infected with Cre retrovirus and sorted for EYFP+ (Cre-activated) DN2 phenotype. Control for experiment 1: wildtype (C57BL/6) DN2 pro-T cells generated in parallel, also treated with Cre retrovirus but sorted only for DN2 phenotype. Control for experiment 2: same genotype as experimental, but infected with a GFP+ empty retroviral vector and sorted for GFP+ DN2 phenotype. Two pairs of RNA-seq samples of DN2 pro-T cells were generated for comparison, each pair consisting of a Gata3-deleted sample plus a stage-matched control.
2014-09-02 | E-GEOD-59215 | biostudies-arrayexpress
Project description:The purpose of the study was to determine what genes in DN2 pro-T cells are immediately regulated by the transcription factor GATA-3, either as activation targets or as repression targets. To do this, two pairs of Gata3-floxed and control pro-T cells were generated and analyzed by RNA-seq within the first day of deletion of the Gata3 gene. Pro-T cells were generated by differentiation in vitro on OP9-DL1 monolayers of fetal liver-derive precursors from wildtype or Gata3-floxed mice, and the Gata3 gene was acutely deleted by transduction with Cre retroviral vector. Within 20 hr after transduction, samples of acutely Gata3-deleted and control DN2 cells were sorted and RNA prepared for RNA-seq analysis. High-throughput sequencing of the samples was carried out. Experimental Gata3 deleted samples in both cases were Gata3-floxed, ROSA26R-EYFP samples infected with Cre retrovirus and sorted for EYFP+ (Cre-activated) DN2 phenotype. Control for experiment 1: wildtype (C57BL/6) DN2 pro-T cells generated in parallel, also treated with Cre retrovirus but sorted only for DN2 phenotype. Control for experiment 2: same genotype as experimental, but infected with a GFP+ empty retroviral vector and sorted for GFP+ DN2 phenotype.
2014-09-02 | GSE59215 | GEO
Project description:Total gene expression analysis was performed on CRE induced conditional knockout E12.5 MEFs relative to GFP infected control MEFs. Intent was to analyze the role of H3f3b in overall gene expression. For conditional KO, three lines of H3f3b FL/FL E12.5 MEFs (cKO1, cKO2 and pcKO1) were transduced with Cre retroviruses and compared to their respective lines of MEFs transduced solely with GFP vector (as control). Total RNA was isolated for gene analysis.
2013-04-11 | E-GEOD-35301 | biostudies-arrayexpress
Project description:Expression data from retroviral vector-infected immortalized mouse embryonic fibroblasts (MEFs)
| PRJNA123117 | ENA
Project description:PA1 has been identified as a component of a MLL3/4-containing histone methyltransferase complex. PA1 directly interacts with PTIP but not with other complex components. Since biological functions of PA1 are unknown, we used microarrays to determine which genes are regulated by PA1. To identify PA1-regulated genes, immortalized PA1 conditional knockout PA1loxP/loxP MEFs were infected with retroviruses expressing either Cre recombinase or vector alone. We prepared duplicated RNAs from either vector or Cre infected cells (PA1+/+ or PA1-/-) for 4 affymetrix microarrays.
2013-12-31 | E-GEOD-20157 | biostudies-arrayexpress
Project description:Transcriptional profiling of primary Cdk7lox/lox MEFs comparing Adeno-Cre vs Adeno-GFP infected controls. Samples were obtained 7 days after the Adeno-Cre mediated elimination of Cdk7. Goal was to determine the effects of Cdk7 elimination on RNA polII-mediated transcription. Two-condition experiment, Adeno-Cre vs. Adeno-GFP infected Cdk7lox/lox MEFs. Biological replicates: 10 independent primary MEF preparations.
2012-04-17 | E-GEOD-36050 | biostudies-arrayexpress
Project description:Histone acetyltransferases (HATs) GCN5/PCAF and CBP/p300 are transcription coactivators. However, how these HATs regulate ligand-induced nuclear receptor target gene expression remains unclear. Here we show in mouse embryonic fibroblasts (MEFs), deletion of GCN5/PCAF specifically eliminates acetylation on H3K9 (H3K9Ac) while deletion of CBP/p300 selectively reduces acetylation on H3K18 and H3K27 (H3K18/27Ac). Treating MEFs with a specific ligand for nuclear receptor PPARdelta induces sequential increases of H3K18/27Ac and H3K9Ac on the promoter of PPARdelta target gene Angptl4, which correlates with a robust ligand-induced Angptl4 expression. Inhibiting transcription elongation blocks ligand-induced H3K9Ac but not H3K18/27Ac on Angptl4 promoter. Finally, we show CBP/p300 and their HAT activities are required, while GCN5/PCAF and H3K9Ac are dispensable, for ligand-induced PPARdelta target gene expression in MEFs. These results highlight the substrate and site specificities of HATs in cells, and suggest that GCN5/PCAF- and CBP/p300-mediated histone acetylations play distinct roles in regulating ligand-induced nuclear receptor target gene expression. PCAF and GCN5 have some redundant function. To identify PCAF/GCN5-regulated genes, immortalized MEFs with PCAF knockout and GCN5 conditional knockout were infected with retroviruses expressing either Cre recombinase or vector alone. We prepared duplicated RNAs from either vector or Cre infected cells (PCAF-/-;GCN5+/- or PCAF-/-;GCN5+/-) and RNAs from either Vector or Cre infected the other independently immortalized cells for 6 affymetrix microarray.
2013-12-31 | E-GEOD-20008 | biostudies-arrayexpress
Project description:In this work, we aimed at studying the impact of microRNAs on antiviral responses, using inducible deletion of one or two copies of Dicer1 (in Dicer-floxed x EsrCRE+ MEFs). Unexpectedly, we discovered that Cre-ERT activation by hydroxytamoxifen (OHT) alone, independent of Dicer1 deletion, had a strong impact on antiviral responses. These microarrays were performed on SV40 immortalized Dicer1 fl/fl EsrCRE+ MEFs, Dicer1 fl/wt EsrCRE+ MEFs, 96 h after initial OHT treatment, and SV40 immortalized Dicer1 wt/wt EsrCRE+ MEFs, Dicer1 wt/wt EsrCRE-neg MEFs (Wild Type MEFs), 48 h after initial OHT treatment. These analyses revealed the strong induction of several antiviral genes (Rsad2, Cxcl10...), following Cre-ERT activation.
2016-05-18 | GSE72024 | GEO