E-MTAB-3971
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-3971 | ExpressionAtlas | 2015-10-22
REPOSITORIES: ExpressionAtlas
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Project description:Constitutively active Stat3 in mouse embryonic fibroblasts (MEFs)
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Project description:Targeted deletion of skNAC in mice resulted in early embryonic lethality with cardiac defects. In order to investigate the molecular mechanism of the cardiac defect, we designed the microarray comparing gene expression of the mutant E11.5 heart to wild type E11.5 heart. Keywords: genetic modification in mouse 3 for each genotypes, comparing Littermates of E11.5, total RNA (500ng) from ventricles, Affymetrix GeneChip Mouse Genome 430 2.0 Array
2010-11-19 | E-GEOD-5841 | biostudies-arrayexpress
Project description:To investigate the function of genes in heart, we performed gene expression microarray for the hearts of 4 sham-operated mice and 4 anterior interventricular artery ligated mice. 4 mice were subjected to permanent occlusion of the anterior interventricular artery while 4 mice were subjected to the identical surgical procedure without coronary ligation. 24 hours after the permanent occlusion, mice were sacrificed and the ventricles of heart were harvested for RNA isolation. Total RNAs were labelled and hybridised on Agilent Mouse SurePrint G3 Array. One sample per array.
2015-04-25 | E-GEOD-46395 | biostudies-arrayexpress
Project description:Analysis of heart ventricles from Hopx, Hdac2, and both Hopx-Hdac2 deficient embryos at embryonic day E16.5. Results provide insight into the role of Hopx and Hdac2 in cardiac development. We used microarrays to detail the global programme of gene expression underlying cardiac development by Hopx and Hdac2 and identified distinct classes of up-regulated and down-regulated genes during this process. Mouse embryonic ventricles were selected at E16.5 for RNA extraction and hybridization on Affymetrix microarrays. We obtained three independent embryonic ventricles for WT, Hopx-null, Hdac2-null, and Hopx-Hdac2 double null genotypes.
2010-08-19 | E-GEOD-23700 | biostudies-arrayexpress
Project description:Goals of this study were to identify new candidates involved in the development of the Atrioventricular cushions in the mouse heart. Keywords = Heart development Keywords = Atrioventricular cushions Keywords = Atrioventricular junction Keywords = Atrioventricular myocardium Keywords = embryonic day ED10.5-11.0 Keywords = ventricles Keywords: development analysis
2007-09-12 | GSE4903 | GEO
Project description:Mammalian heart development is built on highly conserved molecular mechanisms with polygenetic perturbations resulting in a spectrum of congenital heart diseases (CHD). However, the transcriptional landscape of cardiogenic ontogeny that regulates proper cardiogenesis remains largely based on candidate-gene approaches. Herein, we designed a time-course transcriptome analysis to investigate the genome-wide expression profile of innate murine cardiogenesis ranging from embryonic stem cells to adult cardiac structures. This comprehensive analysis generated temporal and spatial expression profiles, prioritized stage-specific gene functions, and mapped the dynamic transcriptome of cardiogenesis to curated pathways. Reconciling the bioinformatics of the congenital heart disease interactome, we deconstructed disease-centric regulatory networks encoded within this cardiogenic atlas to reveal stage-specific developmental disturbances clustered on epithelial-to-mesenchymal transition (EMT), BMP regulation, NF-AT signaling, TGFb-dependent induction, and Notch signaling. Therefore, this cardiogenic transcriptional landscape defines the time-dependent expression of cardiac ontogeny and prioritizes regulatory networks at the interface between health and disease. To interrogate the temporal and spatial expression profiles across the entire genome during mammalian heart development, we designed a time-course microarray experiment using the mouse model at defined stages of cardiogenesis, starting with embryonic stem cells (ESC, R1 stem cell line), early embryonic developmental stages: E7.5 whole embryos, E8.5 heart tubes, left and right ventricle tissues at E9.5, E12.5, E14.5, E18.5 to 3 days after birth (D3) and adult heart (Figure 1A). At each time point, microarray experiments were performed on triplicate biological samples. Starting at E9.5, tissue samples from left ventricles (LV) and right ventricles (RV) were microdissected for RNA purification and microarray analysis to determine spatially differential gene expression between LV and RV during heart development.
2014-05-19 | E-GEOD-51483 | biostudies-arrayexpress
Project description:Inflammation is a major factor in heart disease. IκB kinase (IKK) and its downstream target NF-κB are regulators of inflammation and are activated in cardiac disorders, but their precise contributions and targets are unclear. We analyzed IKK/NF-κB function in the heart by a gain-of-function approach, generating an inducible transgenic mouse model with cardiomyocyte-specific expression of constitutively active IKK2 (IKK2-CA). In adult animals, IKK2 activation led to inflammatory dilated cardiomyopathy and heart failure. Transgenic hearts showed infiltration with CD11b+ cells, fibrosis, fetal reprogramming, and atrophy of myocytes with strong constitutively active IKK2 expression. To gain insight into proximal events after activation of IKK2/NF-κB, we isolated cardiomyocytes and activated the transgene in vitro, thus avoiding interference of other cell types. Gene expression analysis revealed up-regulation of transcripts of chemotactic cytokines, adhesion molecules, and a striking number of IFN-regulated genes in cardiomyocytes expressing IKK2-CA. In addition, apoptotic and anti-apoptotic genes were up-regulated.
2015-10-19 | E-MTAB-3975 | biostudies-arrayexpress
Project description:The snap-frozen mouse heart ventricles that was harvested at ZT6 or ZT18 from both WT and Rev-erb cardiomyocytes specific KO mice were used for metabolomics study.
2021-09-10 | ST001917 | MetabolomicsWorkbench
Project description:The failed heart is characterized by re-expression of a fetal gene program, which contributes to adaptation and maladaptation in heart failure. To define genomewide enhancer and promoter use in heart failure, Cap Analysis of Gene Expression (CAGE-seq) was applied to healthy and failed human left ventricles to define short RNAs associated with both promoters and enhancers. Integration of CAGE-seq data with RNA sequencing identified a combined ~17,000 promoters and ~1,500 enhancers active in healthy and failed human left ventricles. Comparing promoter usage between healthy and failed hearts highlighted promoter shifts which altered amino-terminal protein sequences. Comparing enhancer usage between healthy and failed hearts revealed a majority of differentially utilized heart failure enhancers were intronic and primarily localized within the first intron, identifying this position as a common feature associated with tissue-specific gene expression changes in the heart. This dataset defines the dynamic genomic regulatory landscape underlying heart failure and serves as an important resource for understanding genetic contributions to cardiac dysfunction.
2020-09-01 | GSE147236 | GEO
Project description:Accurate control of tissue-specific gene expression plays a pivotal role in heart development. However, few cardiac transcriptional enhancers have thus far been identified. Extreme non-coding sequence conservation successfully predicts enhancers active in many tissues, but fails to identify substantial numbers of enhancers active in the heart. We used ChIP-seq with the enhancer-associated protein p300 from mouse embryonic heart tissue to identify over three thousand candidate heart enhancers genome-wide. In contrast to other studied tissues at this time-point, most candidate heart enhancers are not deeply conserved in vertebrate evolution. Nevertheless, the testing of 130 candidate regions in a transgenic mouse assay revealed that most of them reproducibly function as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for tissue-dependent differences in evolutionary constraint of enhancers acting through the transcriptional co-activator p300 at this time-point, and identify a large population of poorly conserved heart enhancers. Examination of p300 binding in embryonic stage 11.5 mouse heart and midbrain
2010-08-22 | E-GEOD-22549 | biostudies-arrayexpress