GEO DataSets

(Submitter supplied) In previous studies, we identified and demonstrated that a 1.2kb cebpd downstream element (CEN) is capable and neccessary for the induction of cebpd in the kidney after cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer (CEN) mutant fish zebrafish to massive injuries of the heart.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29008

12 Samples

Download data: TXT

(Submitter supplied) we profiled chromatin accessibility of zebrafish endothelial cells after amputation injury and identify an mmp14b endothelial enhancer induced by heart injury in zebrafish. We show that the enhancer is required for mmp14b expression and regeneration in response to heart injury. Moreover, the enhancer depends on a consensus TEAD-binding motif, suggesting a role for Hippo signaling upstream of mmp14b.

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL14875

9 Samples

Download data: BIGWIG

(Submitter supplied) The goal of this study is to unveal the responses of uninjured tissue to distant tissue injury and the structures required for long-range responses to tissue injuries. we profiled responses by the brain and kidney in zebrafish to massive injuries of the heart and identified cebpd transcript induction in both tissue. We also identified and demonstrated that a 1.2kb cebpd downstream element is capable and neccessary for the induction of cebpd in the brain after cardiac injury.

Organism:

Danio rerio

Type:

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

Platform:

GPL21741

24 Samples

Download data: BW, 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) We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9319

4 Samples

Download data: TXT

(Submitter supplied) We compared transcriptional and chromatin profiles of regenerating zebrafish hearts following genetic ablation with profiles from uninjured zebrafish hearts.

Organism:

Danio rerio

Type:

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

Platforms:

GPL9319 GPL14875

8 Samples

Download data: TXT, WIG

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

Organism:

Danio rerio

Type:

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

Platform:

GPL21741

16 Samples

Download data: BED

(Submitter supplied) We report high-throughput profiling of gene expression from whole zebrafish ventricles. We profile mRNA in uninjured ventricles and those undergoing regeneration 14 days after genetic ablation. 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) We report high-throughput profiling of acetylation of lysine 27 on histone H3 from whole zebrafish ventricles. The H3K27Ac mark has been shown to be present at active enhancer elements and including regions of active chromatin. We profile H3K27Ac in uninjured cardiomyocytes and those undergoing regeneration 14 days after genetic ablation. This study provides a framework for understanding chromatin transitions during adult models of regeneration.

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21741

2 Samples

Download data: BED

(Submitter supplied) We report high-throughput profiling of transgenic histone H3.3 in zebrafish cardiomyocytes. The replacement histone H3.3 is deposited at sites of nucleosome turnover including regions of active chromatin. We profile H3.3 in uninjured cardiomyocytes, those undergoing regeneration 14 days after genetic ablation and those proliferating 7 days after Nrg1 stimulated hyperplasia. This study provides a framework for understanding chromatin transitions during adult models of regeneration.

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21741

10 Samples

Download data: BED

(Submitter supplied) Mammalian genomes likely encode all gene products required to regenerate an amputated limb, yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non-mammalian vertebrates possess these instructions, which exist as gene cis-regulatory elements. Here, to identify candidate tissue regeneration enhancer elements (TREEs) important for zebrafish fin regeneration, we performed ATAC-seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. more...

Organism:

Danio rerio

Type:

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

Platform:

GPL21741

36 Samples

Download data: BW, TXT

(Submitter supplied) Cardiac pacemaker cells (PCs) in the sinoatrial node (SAN) have a distinct gene expression program that allows them to fire automatically and initiate the heartbeat. Although critical SAN transcription factors, including Isl1, have been identified, the cis-regulatory architecture that governs PC-specific gene expression is not understood, and discrete enhancers required for gene regulation in the SAN have not been identified. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL21103

13 Samples

Download data: BW, 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) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

2 Samples

Download data: TXT

(Submitter supplied) In this study, we have applied ChIP-Seq to identify putative regulatory elements throughout the zebrafish genome. For this purpose we identified sequences within the zebrafish genome that associate with H3K4me1 and H3K4me3, which are epigenetic modifications known to be associated with active cis-regulatory elements in other species.

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10164

6 Samples

Download data: BED, WIG

(Submitter supplied) The goal of this study is to compare the transcriptome of heart failure patients (with ischemic or dilated cardiomyopathy) undergoing heart transplantation compared with healthy controls.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16288

36 Samples

Download data: TXT

(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 zebrafish has been widely used for the study of human disease and development, as ~70% of the protein-coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome, however, has lagged behind that of other model systems such as mouse and Drosophila. Based on multi-omics approaches taken in the ENCODE and Roadmap Epigenomics projects, we performed RNA-seq, ATAC-seq, ChIP-seq and Hi-C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. more...

Organism:

Danio rerio

Type:

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

4 related Platforms

204 Samples

Download data: BED, BW, HIC, NARROWPEAK, TXT

(Submitter supplied) The human ether-a-go-go-related gene KCNH2 encodes the voltage-gated potassium channel underlying IKr, a current critical for the repolarization phase of the cardiac action potential. Mutations in KCNH2 that cause a reduction of the repolarizing current can result in cardiac arrhythmias associated with long QT syndrome. Here, we investigated the regulation of this critical cardiac gene and identified multiple active enhancers in the Kcnh2 locus. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

4 Samples

Download data: WIG

(Submitter supplied) H3K27Ac ChIP-seq in wild type and cohesin-deficient thymocytes

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

11 Samples

Download data: BED, WIG