Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA150771 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR400043.fastq.gz | Fastqsanger.gz | |||
| SRR400044.fastq.gz | Fastqsanger.gz | |||
| SRR400045.fastq.gz | Fastqsanger.gz | |||
| SRR400046.fastq.gz | Fastqsanger.gz | |||
| SRR453055.fastq.gz | Fastqsanger.gz |
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Project description:The contraction pattern of the heart relies on the activation and conduction of the electrical impulse. Perturbations of cardiac conduction have been associated with congenital and acquired arrhythmias as well as cardiac arrest. The pattern of conduction depends on the regulation of heterogeneous gene expression by key transcription factors and transcriptional enhancers. Here, we assessed the genome-wide occupation of conduction system–regulating transcription factors TBX3, NKX2-5, and GATA4 and of enhancer-associated coactivator p300 in the mouse heart, uncovering cardiac enhancers throughout the genome. Examination of 3 cardiac transcription factors and p300 in adult mouse heart
2012-06-22 | E-GEOD-35151 | biostudies-arrayexpress
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Project description:The contraction pattern of the heart relies on the activation and conduction of the electrical impulse. Perturbations of cardiac conduction have been associated with congenital and acquired arrhythmias as well as cardiac arrest. The pattern of conduction depends on the regulation of heterogeneous gene expression by key transcription factors and transcriptional enhancers. Here, we assessed the genome-wide occupation of conduction system–regulating transcription factors TBX3, NKX2-5, and GATA4 and of enhancer-associated coactivator p300 in the mouse heart, uncovering cardiac enhancers throughout the genome.
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Project description:Through integration of GATA4 genome-wide occupancy and RNA-seq dataset in embryonic conditional knockout heart, we identified a class of the master cardiac regulator GATA4 bound enhancers. With combinatorial assembly of chromatin signatures, we further refined that a unique type of fetal distal GATA4 enhancers enriched for H3K27ac, H3K4me1, but not for H3K4me3 and RNA polymerase II, are reinstated in adult hypertrophic heart. Study Gata4 and histone modifications in E12.5, Adult, Banding and Sham, and to correlate to gene expression and heart function
2014-08-13 | E-GEOD-52123 | biostudies-arrayexpress
Project description:GATA4 regulates the liver development, but it's function and the gene transcriptional programs it regulates in the adult liver is unknown. In this study, we determined the genome-wide occupancy sites of GATA4 by performing ChIP-seq of whole livers. We have identified 4409 GATA4 enrichment peaks using two peak calling methods and irreproducible discovery rate (IDR) analysis. This corresponds to 3075 genes with GATA4 peaks within -5 kb of transcription start site (TSS) and +5 kb of transcription termination site (TTS). MEME analysis shows that approximately 90% of the peaks have the WGATAR motif, suggesting direct binding by GATA4. The peaks containing the WGATAR motif have a ChIP-seq higher tag enrichment score than peaks lacking the motif. Genome Regions Enrichment of Annotations Tool (GREAT) analysis of genes bound by GATA4 identified ontologies with liver specific functions. In summary, our study shows for the first time genome-wide occupancy profile of GATA4in the adult mouse liver. ChIP-sequencing of whole mouse livers from 2-3 month old mice
2013-11-07 | E-GEOD-49131 | biostudies-arrayexpress
Project description:Through integration of GATA4 genome-wide occupancy and RNA-seq dataset in embryonic conditional knockout heart, we identified a class of the master cardiac regulator GATA4 bound enhancers. With combinatorial assembly of chromatin signatures, we further refined that a unique type of fetal distal GATA4 enhancers enriched for H3K27ac, H3K4me1, but not for H3K4me3 and RNA polymerase II, are reinstated in adult hypertrophic heart.
2014-08-13 | GSE52123 | GEO
Project description:GATA4 regulates the liver development, but it's function and the gene transcriptional programs it regulates in the adult liver is unknown. In this study, we determined the genome-wide occupancy sites of GATA4 by performing ChIP-seq of whole livers. We have identified 4409 GATA4 enrichment peaks using two peak calling methods and irreproducible discovery rate (IDR) analysis. This corresponds to 3075 genes with GATA4 peaks within -5 kb of transcription start site (TSS) and +5 kb of transcription termination site (TTS). MEME analysis shows that approximately 90% of the peaks have the WGATAR motif, suggesting direct binding by GATA4. The peaks containing the WGATAR motif have a ChIP-seq higher tag enrichment score than peaks lacking the motif. Genome Regions Enrichment of Annotations Tool (GREAT) analysis of genes bound by GATA4 identified ontologies with liver specific functions. In summary, our study shows for the first time genome-wide occupancy profile of GATA4in the adult mouse liver.
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Project description:The second heart field (SHF) comprises a population of mesodermal progenitor cells that are added to the nascent linear heart to give rise to the majority of the right ventricle, interventricular septum, and outflow tract of mammals and birds. The zinc finger transcription factor GATA4 functions as an integral member of the cardiac transcription factor network in the SHF and its derivatives. In addition to its role in cardiac differentiation, GATA4 is also required for cardiomyocyte replication, although the transcriptional targets of GATA4 required for proliferation have not been previously identified. In the present study, we disrupted Gata4 function exclusively in the SHF and its derivatives. Gata4 SHF knockout mice die by embryonic day 13.5 and exhibit hypoplasia of the right ventricular myocardium and interventricular septum and display profound ventricular septal defects. Loss of Gata4 function in the SHF results in decreased myocyte proliferation in the right ventricle, and we identify numerous cell cycle genes that are dependent on Gata4 by microarray analysis. We show that Gata4 is required for Cyclin D2 expression in the right ventricle and that the Cyclin D2 promoter is bound and activated by GATA4 via three consensus GATA binding sites. These findings establish Cyclin D2 as a direct transcriptional target of GATA4 and support a model in which GATA4 controls cardiomyocyte proliferation by coordinately regulating numerous cell cycle genes. Experiment Overall Design: Onewat ANOVA with post-hoc was done with 3 genotypes with replicates. Three genetypes are Gata4flox/+; Nkx2-5+/+ (control, n=3), Gata4flox/+; Nkx2-5Cre/+ (Gata4; Nkx2-5 double heterozygous, Experiment Overall Design: 170 n=3), and Gata4flox/flox; Nkx2-5Cre/+ (Gata4 CKONkx, n=5).
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Project description:[1] Gene expression profiling in Gata4, Mef2a knockdown in HL-1 cells. HL-1 cells infected with adenovirus expressing either control siRNA or Gata4, and Gata4 & Mef2a siRNA. [2] Genome-wide maps of cardiac transcription factors binding region in HL-1 cells. We performed bio-ChIP-seq using streptavidin beads immunoprecipitation of biotinylated 5 cardiac transcription factors (fbio) and P300 antibody ChIP-seq. We used a dox-inducible dual adenovirus system to express biotinylated Core Cardiac TFs in HL1. One adenovirus expressed the dox-activated reverse tet activator protein (rtTA) and the E. coli biotinylating enzyme BirA from the cardiac specific rat troponin T promoter. The second virus expressed a Core Cardiac TF fused to a C-terminal flag-bio epitope tag, where bio is the 15 amino acid substrate for BirA. This in vivo biotinylation approach permits pulldown of different factors to be performed under identical, stringent conditions, and circumvents limitations posed by available antibodies. We titrated adenovirus and dox doses to express GATA4flbio and MEF2Aflbio at near endogenous levels. The same conditions were then used to express SRFflbio, TBX5flbio, and NKX2-5flbio. Reference: 12. de Boer E, Rodriguez P, Bonte E, Krijgsveld J, Katsantoni E et al. (2003) Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc Natl Acad Sci U S A 100: 7480-7485. [1] Gene expression profiling: Identify differentially expressed genes after siRNA Gata4 or Gata4_Mef2a double knockdown in HL-1 cells [2] Genome occupancy profiling: Identify cardiac active enhancers by identified 5 cardiac transcription factors and P300 peaks.
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