GEO DataSets

(Submitter supplied) We report high-throughput profiling of gene expression from whole zebrafish ventricles. We profile mRNA in uninjured ventricles and those undergoing 7 days of cardiomyocyte hyperplasia after genetic stimulation of Nrg1. This study provides a framework for understanding transcriptional changes during adult models of regeneration.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

4 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) Animals possess control mechanisms to synchronize organ and organismal size during growth, to maintain tissue integrity through homeostatic cell proliferation, and to counter major injury with regeneration. A principal research goal is to elucidate mitogenic triggers that underlie these mechanisms. Here, from a large-scale in vivo chemical screen, we discovered that analogues of the essential nutrient vitamin D potently activate heart muscle cell division in larval zebrafish. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

4 Samples

Download data: TXT

(Submitter supplied) A transgenic line cmlc2:TRAP was made to express EGFP-fused ribosomal protein L10a (EGFP-L10a) in zebrafish cardiomyocytes. Then ribosome-associated RNAs were immuoprecipitated from uninjured and injured adult cmlc2:TRAP fish to determine the differential expression changes during zebrafish heart regeneration.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL17210

9 Samples

Download data: PAIR

(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) 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) The study compares gene expression profile at 20 days post amputation of the zebrafish ventricular heart between dusp6 mutant and WT siblings.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

4 Samples

Download data: XLSX

(Submitter supplied) In contrast to mammals, zebrafish regenerate heart injuries via proliferation of cardiomyocytes located at the wound border. Here, we show that tomo-seq can be used to identify whole-genome transcriptional profiles of the injury zone, the border zone and the healthy myocardium. Interestingly, the border zone is characterized by the re-expression of embryonic cardiac genes that are also activated after myocardial infarction in mouse and human, including targets of Bone Morphogenetic Protein (BMP) signaling. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

2 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) To better understand the possible mechanisms that vegfaa mutants display to compensate for the lack of vegfaa, we performed transcriptomic profiling of vegfaa+/+ and vegfaa-/- ventricles. Total RNA was isolated from hearts extracted from vegfaa+/+ and vegfaa-/- fish (8 months old) pooling 4 hearts per sample.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL20686

2 Samples

Download data: TXT

(Submitter supplied) Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms, such as zebrafish, cardiac injury is followed by transient fibrosis and scar-free regeneration. The mechanisms that drive scarring versus scar-free regeneration are not well understood. Here, we show that the homeobox-containing transcription factor Prrx1b is required for scar-free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

4 Samples

Download data: CSV, TSV

(Submitter supplied) As Grl/Hey2 directly binds DNA through E box motifs and mediates transcription repression, we aim to gain insights into potential target genes of Grl/Hey2 during heart regeneration. We performed RNA-seq analyses using total RNAs collected from 4-HT-treated Tg(cmlc2:creER;cmlc2:nRSGG) hearts and Tg(cmlc2:nRSGG) control hearts, as well as grl5nt-/- mutant hearts and wild-type hearts following ventricular resection at 7 dpa. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

12 Samples

Download data: XLS, XLSX

(Submitter supplied) Primary neonatal rat cardiac myocytes or fibroblasts were isolated and subjected to siRNA mediated Yap knockdown

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24782

12 Samples

Download data: XLSX

(Submitter supplied) A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24776

12 Samples

Download data: XLSX

(Submitter supplied) we are comparing sham-injured zebrafish heart samples with 4 days post cryoinjured zebrafish heart samples.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL14664

1 Sample

Download data: TXT

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

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20828 GPL30614

3 Samples

Download data: MTX, TSV

(Submitter supplied) In contrast to adult mammals, adult zebrafish are able to fully regenerate injured cardiac tissue, and this regeneration process requires an adequate and tightly controlled immune response. However, which immune aspects drive particular aspects of the regenerative response are unclear. Here, we report the participation and requirement of the antigen presentation-adaptive immunity axis during zebrafish cardiac regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

1 Sample

Download data: TSV

(Submitter supplied) In contrast to adult mammals, adult zebrafish are able to fully regenerate injured cardiac tissue, and this regeneration process requires an adequate and tightly controlled immune response. However, which immune aspects drive particular aspects of the regenerative response are unclear. Here, we report the participation and requirement of the antigen presentation-adaptive immunity axis during zebrafish cardiac regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

2 Samples

Download data: MTX, TSV

(Submitter supplied) In contrast to adult mammals, adult zebrafish are able to fully regenerate injured cardiac tissue, and this regeneration process requires an adequate and tightly controlled immune response. However, which immune aspects drive particular aspects of the regenerative response are unclear. Here, we report the participation and requirement of the antigen presentation-adaptive immunity axis during zebrafish cardiac regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

4 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