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ATAC-seq on endothelial cells from E11.5 mouse hearts

ABSTRACT: ATAC-seq on endothelial cells from E11.5 mouse hearts

PROVIDER: PRJEB11459 | ENA |

REPOSITORIES: ENA

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ChIP-seq of Tbx20 tagged with GFP in E11.5 mouse hearts

Project description:ChIP-seq of Tbx20 tagged with GFP in E11.5 mouse hearts

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ATAC-seq on endocardial cells from E12.5 mouse hearts in Tbx20 knockouts and wild type counterparts

Project description:We used ATAC-seq (Buenrostro et al, 2013) to identify regions of open chromatin in FACS sorted mouse endothelial cells from E12.5 hearts. Please note that the animals were injected at different dates, which resulted in different effects of the knockout, as indicated in the batch attribute of the samples. This data set is part of the study \Endocardial Tbx20 is essential for mesenchymal and myocardial cell movements required for cardiac septation\. Peaks were called using HOMER (-gsize 1.87e9 -region -tbp 1). Replicate 1: -fdr 1e-8, replicate 2: default parameters. Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10: 12138.

2017-06-02 | E-MTAB-3972 | biostudies-arrayexpress

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Genome-wide analysis of epicardial gene expression in E11.5 mouse hearts

Project description:Identification of epicardium-enriched genes in the embryonic heart. The epicardium encapsulates the heart and functions as a source of multipotent progenitor cells and paracrine factors essential for cardiac development and repair. Injury of the adult heart results in re-activation of a developmental gene program in the epicardium, but the transcriptional basis of epicardial gene expression has not been delineated. We established a mouse embryonic heart organ culture and gene expression system that facilitated the identification of epicardial enhancers activated during heart development and injury. Epicardial activation of these enhancers depends on a combinatorial transcriptional code centered on CCAAT/enhancer binding protein (C/EBP) transcription factors. Disruption of C/EBP signaling in the adult epicardium reduced injury-induced neutrophil infiltration and improved cardiac function. These findings reveal a transcriptional basis for epicardial activation and heart injury, providing a platform for enhancing cardiac regeneration. Total RNA obtained from lacZ-positive epicardial cells isolated from the E11.5 Tcf21lacZ hearts compared to total dissociated heart cells

2012-11-01 | E-GEOD-41959 | biostudies-arrayexpress

Expression data from Shox2 knockout and wildtype right atria of E11.5 mouse hearts

Project description:The heartM-bM-^@M-^Ys rhythm is initiated and regulated by a group of specialized cells in the sinoatrial node (SAN), the primary pacemaker of the heart. Abnormalities in the development of the SAN can result in irregular heart rates (arrhythmias). Although several of the critical genes important for SAN formation have been identified, our understanding of the transcriptional network controlling SAN development remains at a relatively early stage. The homeodomain transcription factor Shox2 plays an essential early role in the specification and patterning of the SAN. Here, we compared gene expression levels in the right atria of wildtype and Shox2-/- hearts using microarray experiments to identify Shox2 target genes. Right atria of E11.5 mouse embryos were dissected and genotyped for RNA extraction. RNA from 6 embryos and 2 independent pregnancies was pooled per genotype (Wildtype and Shox2 Knockout) and compared.

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Project description:Purpose: The goal of this study is to identify the differential cardiac chromatin accessibility between WT and cardiomyocyte conditional knockout (Chd4-CMko) hearts at E10.5 using ATAC-seq. Methods: Three hearts at E10.5 were pooled per genotype per replicate, and were then dissociated into single cells. 40,000 viable cells were taken for were lysed to isolate nuclei, which were treated with Tn5 transposase (Nextera DNA Sample Prep Kit, Illumina) to isolate DNA. Fragmented DNA was then amplified using bar-coded PCR primers and libraries were seuqenced. Results: 15736 differential peaks (2-fold change) were identified between E10.5 WT and Chd4-CMko hearts.

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Small RNA analysis of wildtype Mouse embryo and Adar1 null mouse embryo at E11.0 and E11.5 together with mRNA-seq results of E11.5

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