GEO DataSets

(Submitter supplied) Purpose: Studying the epicardium-myocardium crosstalk in the zebrafish larval heart. To do so, we aimed to identify, with RNA-seq, the genes dysregulated following the loss of the epicardial marker gene tcf21 in sorted epicardial cells and cardiomyocytes. Results: We first analyzed the transcriptome of epicardial and myocardial WT cells and identified cell-type specific/enriched genes. Then, we identified several differential expressed genes in tcf21 mutants, including several ligand-receptor couples known to mediate the epicardium-myocardium crosstalk.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24995 GPL18413

15 Samples

Download data: BED, BW

(Submitter supplied) During cardiac development, cells from the precardiac mesoderm fuse to form the primordial heart tube, which then grows by addition of further progenitors to the venous and arterial poles. In the zebrafish, wilms tumor 1 transcription factor a (wt1a) and b (wt1b) are expressed in the pericardial mesoderm at the venous pole of the forming heart tube. The pericardial mesoderm forms a single layered mesothelial sheet that contributes to further the growth of the myocardium, and forms the proepicardium. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24995

6 Samples

Download data: BED, BW

(Submitter supplied) During cardiac development, cells from the precardiac mesoderm fuse to form the primordial heart tube, which then grows by addition of further progenitors to the venous and arterial poles. In the zebrafish, wilms tumor 1 transcription factor a (wt1a) and b (wt1b) are expressed in the pericardial mesoderm at the venous pole of the forming heart tube. The pericardial mesoderm forms a single layered mesothelial sheet that contributes to further the growth of the myocardium, and forms the proepicardium. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

9 Samples

Download data: CSV

(Submitter supplied) The epicardium, a thin mesothelial tissue layer that encompasses the heart, is a dynamic structure that is essential for cardiac regeneration in species with elevated regenerative capacity like zebrafish. To dissect epicardial cell states and associated pro-regenerative functions, we performed single-cell RNA-sequencing and identified 7 epicardial cell clusters in adult zebrafish, with 3 of these clusters enhanced during regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

2 Samples

Download data: MTX, TSV

(Submitter supplied) The goal of the present study is to determine the miRNA cargo present in epicardial extracellular vesicles. For that, epicardial cells and human primary epicardial cells were cultured. Conditioned media was isolated from mouse epicardial cells and human primary epicardial cells derived from right atrial appendages in two different states: “cobble” (inactive) cells and “spindle” (active) . RNA from EVs was isolated and sequenced to determine the miRNA content profile.

Organism:

Mus musculus; Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21103 GPL20301

6 Samples

Download data: TXT

(Submitter supplied) By contrast with mammals, adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source, and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential, the extent of cellular heterogeneity within epicardial tissue is largely unexplored. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

40 Samples

Download data: TXT

(Submitter supplied) Complex interplay between cardiac tissues is crucial for their integrity. The flow responsive transcription factor KLF2, which is expressed in the endocardium, is vital for cardiovascular development but its exact role remains to be defined. To this end, we mutated both klf2 paralogues in zebrafish, and while single mutants exhibit no obvious phenotypes, double mutants display a novel phenotype of cardiomyocyte extrusion towards the abluminal side. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL19785

2 Samples

Download data: TXT

(Submitter supplied) Purpose:to identify with transcriptomic analysis, gene targets of Vegfc signaling during cardiac regeneration in zebrafish. Results: We were able to identify several differential expressed genes, many of which encode for immune related genes, as well as ECM components.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

4 Samples

Download data: TXT

(Submitter supplied) The epicardium is a mesothelial tissue layer that envelops the heart. Cardiac injury activates dynamic gene expression programs in epicardial tissue, which in the case of zebrafish enables subsequent regeneration through paracrine and vascularizing effects. To identify tissue regeneration enhancer elements (TREEs) that control injury-induced epicardial gene expression during heart regeneration, we profiled transcriptomes and chromatin accessibility in epicardial cells purified from regenerating zebrafish hearts. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL14875 GPL21741

18 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Adult zebrafish regenerate heart muscle after severe cardiac damage without significant scarring. The epicardium, a mesothelial cell sheet covering the vetebrate heart, is activated by injury and supports muscle regeneration through paracrine effects and as a source of multipotent cells. The understudied cellular heterogeneity of the adult epicardium during heart regeneration has constrained the effort in mobilizing the epicardium for heart repair. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

3 Samples

Download data: MTX, TSV

(Submitter supplied) Purpose: To compare NGS-derived transcriptome profiling (RNA-seq) between Wild Type and Ptprz1-/- LMVEC and identify transcripts that may be linked to the phenotypic differences observed. Methods: Total RNA from freshly cultured LMVEC was extracted using the NucleoSpin RNA Plus kit from Macherey-Nagel and the concentration and purity was assessed by Nanodrop and gel agarose 1% in TBE 0.5x. RNA from 3 independent fresh cell isolations from the Ptprz1+/+ and the Ptprz1-/- LMVEC was extracted and sent for RNAseq analysis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: TXT

(Submitter supplied) Single cell RNAseq of a model of epicardium derived from human pluripotent stem cell (hPSC-epi) reveals that distinct epicardial sub-populations are defined by high levels of expression for the transcription factors BNC1 and TCF21. Cells positive for the transcription factor WT1 are included in the BNC1 population, which confirms the heterogeneity observed in the mouse with TCF21 and WT1. Analysis of genes differentially expressed between the two populations suggests differences in their biological activities. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

362 Samples

Download data: CSV

(Submitter supplied) During heart regeneration in the zebrafish, fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre-existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here, using sox10 genetic fate mapping, we identified a subset of pre-existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively after cryoinjury. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23274

25 Samples

Download data: TXT

(Submitter supplied) While the heart regenerates poorly in mammals, efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration, resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However, there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

4 Samples

Download data: CSV, TSV

(Submitter supplied) Unlike the adult mammalian heart, which has limited regenerative capacity, the zebrafish heart can fully regenerate following injury. Reactivation of cardiac developmental programmes is considered key to successfully regenerating the heart, yet the regulatory elements underlying the response triggered upon injury and during development remain elusive. Organ-wide activation of the epicardium is essential for zebrafish heart regeneration and is considered a potential regenerative source to target in the mammalian heart. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20828

25 Samples

Download data: TXT

(Submitter supplied) Purpose: identifying, with RNA-seq, genes targets of Snai1b during zebrafish cardiac development. Results: we identified several differential expressed genes, in particular cytoskeletal genes. In particular, the intermediate filament gene desmin b is upregulated.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

4 Samples

Download data: TXT

(Submitter supplied) Transcriptome sequencing of uninjured and regenerating (7dpi) tp53M214K and tp53WT ventricles.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24776

12 Samples

Download data: TXT

(Submitter supplied) Despite extensive studies on endogenous heart regeneration within the past 20 years, the players involved in initiating early regeneration events are far from clear. Here, we assessed the function of neutrophils, the first-responder cells to tissue damage, during heart regeneration. We detected rapid neutrophil mobilization to the injury site after ventricular amputation, peaking at 1-day post-amputation (dpa) and resolving by 3 dpa. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

1 Sample

Download data: MTX, TSV

(Submitter supplied) To delineate the role of the epicardium, the initial site of presentation of the ACM phenotype, the Dsp gene, encoding desmosome protein desmoplakin (DSP) was conditionally deleted in the mouse epicardial cells under the transcriptional regulation of Wilms tumor 1 (Wt1) locus. Single cell RNA sequencing (scRNA-Seq) of ~ 40,000 tagged epicardial-derived cells (EDCs), isolated using the dual reporter R26mT/mG mice, showed an increased number of EDCs expressing unique molecular identifiers of fibroblasts as well as a unique subset of epicardial-derived fibroblasts expressing pro-fibrotic genes in the Wt1-Cre: R26mT/mG: Dsp mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: CSV, MTX, TXT