GEO DataSets

(Submitter supplied) The adult mammalian heart heals after myocardial infarction (MI) by deposition of scar tissue, leading to downstream arrhythmia, remodelling and heart failure1. In contrast, adult zebrafish and neonatal mouse hearts are capable of regenerating after injury. Macrophages are key mediators of tissue repair and appear to be required for both regeneration and healing by scar formation, but the mechanisms underlying these distinct roles are poorly understood2-4. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

28 Samples

Download data: XLS

(Submitter supplied) Canonical roles for macrophages in mediating the fibrotic response after a heart attack (myocardial infarction) include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition. Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

21 Samples

Download data: BW, TXT

(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) Runx1 is a transcription factor that plays a key role in determining the proliferative and differential state of multiple cell types, during both development and adulthood. Here, we report how runx1 is specifically upregulated at the injury site during zebrafish heart regeneration, but unexpectedly, absence of runx1 results in enhanced regeneration. Using single cell sequencing, we found that the wild-type injury site consists of Runx1-positive endocardial cells and thrombocytes that express smooth muscle and collagen genes without differentiating into myofibroblasts. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

3 Samples

Download data: H5

(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) Cardiovascular disease is the leading cause of morbidity and mortality in the Western world due to a limited regenerative capacity. In lieu of new muscle synthesis, the human heart replaces necrotic tissue with deposition of a non-contractile scar. In contrast, the adult zebrafish is endowed with a remarkable regenerative capacity, capable of de novo cardiomyocyte (CM) creation and scar tissue resolution when challenged with an acute injury. more...

Organism:

Danio rerio

Type:

Non-coding RNA profiling by array

Platform:

GPL21083

6 Samples

Download data: TXT

(Submitter supplied) Autonomic drive plays a pivotal role in cardiac regeneration. Sympathetic or cholinergic denervation impairs myocardial regrowth in neonatal mouse and zebrafish hearts. Here, we uncovered the mechanistic underpinning of adrenergic signaling in regenerative repair of the heart to be critically dependent on immunomodulation. Through pharmacological and genetic manipulations, we identified adrenergic receptor alpha-1 as a key regulator of macrophage phenotypic diversification following myocardial infarction in zebrafish. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

2 Samples

Download data: MTX, TSV

(Submitter supplied) Midkine-a is a cytokine that is highly expressed in the heart upon injury that its role in regeneration has not been identified. We generated a KO zebrafish lines, mdkacn105, and studied the effect of mdka deletion in zebrafish adult heart regeneration. By combining histology and high-throughput genomics, we found that loss of mdka leads to arrest of heart regeneration. Mdka mutant hearts display increased collagen deposition in the site of the injury and decreased proliferation of the coronary endothelial cells due to increased expression of ECM including collagen and periostin as well as decreased expression of Hif1a. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

6 Samples

Download data: TXT

(Submitter supplied) Ly6Clow macrophages promote scar formation and prevent early infarct expansion after myocardial infarction (MI). Although CD4+ T cells influence the regulation of Ly6Clow macrophages after MI, the mechanism remains largely unknown. Here, we focused on IL-21 and uncovered its physiological relevance in post-MI hearts. CD4+ T cells harvested from the infarcted heart produce IL-21 upon stimulation, and IL-21 receptor was expressed on Ly6Clo macrophages in the infarcted heart. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

8 Samples

Download data: TXT

(Submitter supplied) Adult zebrafish are able to regenerate many organs such as their caudal fin in only few days post amputation. To explore the landscape and dynamic of the genes involed in regeneration, we performed a global transcriptomic analysis using RNA-seq during zebrafish caudal fin regeneration.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24788

12 Samples

Download data: XLSX

(Submitter supplied) Macrophages play an essential role in tissue regeneration. However, the ability to dissect the role of macrophages in regeneration from their role in wound healing with scar has been hampered by a lack of comparative systems. In this study, we use a mammalian model of tissue regeneration and scar formation to contrast the role of macrophages in both wound healing paradigms. The African Spiny mouse (A. more...

Organism:

Mus musculus; Acomys cahirinus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29848 GPL24247

10 Samples

Download data: MTX, TSV

(Submitter supplied) The gradual decline of tissue functionality is the main reason why humans suffer from age-related diseases. The prevalence for cardiovascular diseases increases with increasing age. In order to prevent age-related cardiac diseases, it is of importance to understand the respective age-associated risk factors. We have therefore compared the ventricular transcriptome of old and young hearts of the model organism zebrafish. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

6 Samples

Download data: CSV

(Submitter supplied) Adult zebrafish have the capacity to regenerate craniofacial ligament tissue following a complete transection injury. How this robust skeletal regeneration is achieved remains undefined. Here, we use single cell RNA sequencing to profile RNA expression from FACS sorted cranial neural crest lineage and non-cranial neural crest lineage cells (including skin and immune populations) in the first 3 days after ligament injury.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

10 Samples

Download data: MTX, TSV