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Single-cell chromatin landscape of non-myocytes reveals AP-1 as a key transcriptional regulator contributing to highly cooperative networks among non-myocyte subtypes during zebrafish heart regeneration [scATAC-seq]

ABSTRACT: Single-cell chromatin landscape of non-myocytes reveals AP-1 as a key transcriptional regulator contributing to highly cooperative networks among non-myocyte subtypes during zebrafish heart regeneration [scATAC-seq]

PROVIDER: PRJNA891665 | ENA |

REPOSITORIES: ENA

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Single-cell chromatin landscape of non-myocytes reveals AP-1 as a key transcriptional regulator contributing to highly cooperative networks among non-myocyte subtypes during zebrafish heart regeneration

Project description:Single-cell chromatin landscape of non-myocytes reveals AP-1 as a key transcriptional regulator contributing to highly cooperative networks among non-myocyte subtypes during zebrafish heart regeneration

| PRJNA891655 | ENA

| PRJNA891666 | ENA

| PRJNA1044716 | ENA

Single Cell Transcriptome Profiling of Cardiac Non-myocyte

Project description:The mammalian heart is composed of a variety types of cells that can be roughly categorized into cardiomyocytes and non-myocytes. Instead of being bystanders of cardiac function, cardiac non-myocytes provide critical structural, mechanical and electrophysiological support to the working myocardium. However, the precise cellular identity and molecular features of the non-myocytes at single cell level remain elusive. Depiction of epigenetic landscape with transcriptomic signatures using the latest single cell multi-omics has the potential to unravel the molecular programs of cardiac non-myocytes underlying their cellular diversity. To characterize the molecular and cellular features of cardiac non-myocytes populations in the adult murine heart at single cell level. We applied single cell Assay for Transposase Aaccessible Chromatin using sequencing (scATAC-seq) in combination with high-throughput single cell RNA-seq (scRNA-seq) to map the epigenetic landscape and gene expression program of cardiac non-myocytes from adult murine heart. Through integrated dual-omics data analysis, we categorize the cardiac non-myocytes into 4 defined populations including endothelial cells, fibroblast, pericytes and immune cells with distinct chromatin accessibility patterns. Cis- and trans-regulatory factors for each cell type were identified. In particular, unbiased sub-clustering and functional annotation of the cardiac fibroblast (FB), indicated the heterogeneity and functionality of FB subtypes associated with cellular response, cytoskeleton organization and immune regulation. We further validated the expression and function of novel markers in major FB sub-populations and experimentally determined the distribution of the FB sub-populations in healthy and injured murine heart. In summary, we comprehensively characterized the non-myocyte cellular identity at the single-cell level and defined FB subpopulations by their functional states.

2021-04-21 | GSE157444 | GEO

Single Cell Epigenome Profiling of Cardiac Non-myocyte

2021-04-21 | GSE157445 | GEO

Fibronectin Induced Cardiac Myocyte Hypertrophy

Project description:Gene expression changes in neonatal rat ventricular myocytes plated in fibronectin (2 samples) or uncoated plates (2 samples). Keywords = Hypertrophy Cardiac Myocyte Fibronectin Keywords: repeat sample

2004-08-19 | GSE1055 | GEO

Mapping the cellular and molecular landscape of cardiac non-myocytes in murine type-2 diabetes

Project description:Here we define key single-cell transcriptional alterations within cardiac non-myocytes, from ventricles of spontaneously type-2 diabetic (db/db) and control (db/h) mouse hearts ([B6.BKS(D)-Lepr<db>/J], stock #000697). The cell preparation sequenced consisted of metabolically active, live and nucleated non-myocyte cells, which were depleted of endothelial cells. The objective of this experiment was to develop a framework for understanding the dynamics of cardiac cell networks in murine type-2 diabetes, as a resource for future mechanistic studies.

2022-11-29 | E-MTAB-11940 | biostudies-arrayexpress

RNA-sequencing of healthy human skeletal myocytes

Project description:Skeletal myocytes are metabolically active and susceptible to insulin resistance, thus implicated in type 2 diabetes (T2D). This complex disease involves systemic metabolic changes and their elucidation at the systems level requires genome-wide data and biological networks. Genome-scale metabolic models (GEMs) provide a network-context to integrate high-throughput data. We generated myocyte-specific RNA-seq data and investigated their correlation with proteome data. These data were then used to reconstruct a comprehensive myocyte GEM. Next, we performed a meta-analysis of six studies comparing muscle transcription in T2D versus healthy subjects. Transcriptional changes were mapped on the myocyte GEM, revealing extensive transcriptional regulation in T2D, particularly around pyruvate oxidation, branched-chain amino acid catabolism, and tetrahydrofolate metabolism, connected through the down-regulated dihydrolipoamide dehydrogenase. Strikingly, the gene signature underlying this metabolic regulation successfully classifies the disease state of individual samples, suggesting that regulation of these pathways is a ubiquitous feature of myocytes in response to T2D. Isolated skeletal muscle precursor cells from six normal glucose tolerant and non-obese males and females were differentiated in vitro. RNA from fully differentiated myotubes was sequenced using RNA-seq.

2015-04-07 | E-GEOD-63887 | biostudies-arrayexpress

Gene expression after knockdown of transcription factors in human iPSC-derived cardiac myocytes

Project description:We report gene expression changes after knockdown of transcription factors in human iPSC-derived cardiac myocytes. In prior experiments we showed that transcription factors known to be important for cardiac development were frequently up-regulated (i.e., "responsive") after small molecule perturbations of cultured iPSC-derived cardiac myocytes. We used RNA sequencing to test whether siRNA-mediated knockdown of transcription factors with different perturbation-responsiveness and tissue-specificity profiles would lead to inappropriate up-regulation of non-myocyte gene sets in cardiac myocytes.

2021-02-17 | GSE166823 | GEO

Transcription profiling of H2O2 treated rat cardiac myocytes

Project description:Title: Changes in gene expression affected by H2O2 in cardiac myocytes. Description: We aim to identify the changes in gene expression in response to oxidative stress in rat neonatal ventricular myocytes. Oxidative stress will be induced by dosing neonatal ventricular myocyte cultures with 0.2, 0.1 and 0.04mM hydrogen peroxide at 2, 4 and 8 hr time points using unstimulated myocytes as control.

2011-11-08 | E-MIMR-12 | biostudies-arrayexpress

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