GEO DataSets

(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) 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) 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) 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) 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) 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) 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) The zebrafish has emerged as a powerful model to study cardiac regeneration; however, the mechanisms by which cardiomyocytes respond to damage by disassembling sarcomeres, proliferating, and repopulating the injured area remain unclear. Here, we show that AP-1 transcription factors play an essential role in regulating the cardiomyocyte response. Using ATAC-Seq, we first find that the cardiomyocyte chromatin accessibility landscape is dynamic following cryoinjury, and that AP-1 motifs are the most highly enriched in regions that gain accessibility during regeneration. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20828

14 Samples

Download data: TXT

(Submitter supplied) Purpose: The goal of this study is to compare transcriptome level between 4 dpci wild-type and ccn2a-/- zebrafish cardiac ventricle. Methods: 4-days-post cryoinjured cardiac ventricular mRNA profiles of wild-type (WT) and cellular communication network factor 2a mutant (ccn2a−/−) zebrafish were generated by deep sequencing, in duplicate. Results: 7 genes showed differential expression between the WT and ccn2a−/− heart, with a fold change ≥1.5 and p value <0.05. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

4 Samples

Download data: TXT

(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) Unlike human hearts, zebrafish hearts efficiently regenerate after injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study, we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery, supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15583

16 Samples

Download data: TXT

(Submitter supplied) We used high throughput sequencing to identify differential expression in siblings, hhex mutants and hhex-overexpression endothelial cells at 48 hpf.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

6 Samples

Download data: TXT

(Submitter supplied) The zebrafish heart remarkably regenerates after a severe ventricular damage followed by inflammation, fibrotic tissue deposition and removal concomitant with cardiac muscle replacement. We have investigated the role of the endocardium in this regeneration process. 3D-whole mount imaging in injured hearts revealed that GFP-labelled endocardial cells in ET33mi-60A transgenic fish become rapidly activated and highly proliferative at 3 days post cryoinjury (dpci). more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15583

6 Samples

Download data: CSV

(Submitter supplied) Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space, and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23274

1109 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) 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate, with 6 brains used per samples.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

6 Samples

Download data: CSV, TXT

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

Organism:

Homo sapiens; Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL14875 GPL18573

20 Samples

Download data

(Submitter supplied) The development of a differentiated and functional vasculature requires coordinated control of cell fate specification, lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels, we uncovered a mutant for the RNA helicase Ddx21. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: CSV

(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) 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