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Links from GEO DataSets

Items: 20

1.

Single-cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.

(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
Series
Accession:
GSE139218
ID:
200139218
2.

Cardiomyocyte heterogeneity in zebrafish development and regeneration

(Submitter supplied) Contrary to adult mammals, zebrafish are able to regenerate their heart after cardiac injury. This regenerative response relies, in part, on the endogenous ability of cardiomyocytes (CMs) to dedifferentiate and proliferate to replenish the lost muscle. However, CM heterogeneity and population dynamics during development and regeneration remain poorly understood. Through comparative transcriptomic analyses of the developing and adult zebrafish heart, we identified tnnc2 and tnni4b.3 expression as markers for CMs at early and late developmental stages, respectively. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20828
4 Samples
Download data: TXT
Series
Accession:
GSE157662
ID:
200157662
3.

Genome–wide transcriptional profiling with spatial resolution identifies Bone Morphogenetic Protein signaling as essential regulator of zebrafish cardiomyocyte regeneration.

(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
Series
Accession:
GSE74652
ID:
200074652
4.

Pre-existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish 

(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
Series
Accession:
GSE133571
ID:
200133571
5.

Gene expression analysis of Nrg1 stimulated zebrafish hearts [mRNA]

(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
Series
Accession:
GSE168371
ID:
200168371
6.

Vitamin D globally accelerates growth and regeneration in zebrafish

(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
Series
Accession:
GSE112826
ID:
200112826
7.

Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration

(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
Series
Accession:
GSE146859
ID:
200146859
8.

Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development

(Submitter supplied) Through analyzing RNA-seq datasets in zfpm1 mutant embryo (36hpf) and maturing heart (21 dpf), we characterized the effects of loss of zfpm1 on the transcriptomic landscape.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23085
8 Samples
Download data: TXT
Series
Accession:
GSE95118
ID:
200095118
9.

Gene expression arrays of cardiomyocyte ribosome-associated RNAs during zebrafish heart regeneration

(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
Series
Accession:
GSE48914
ID:
200048914
10.

Zebrafish heart regeneration

(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
Series
Accession:
GSE90595
ID:
200090595
11.

hapln1 defines an epicardial cell subpopulation that establishes cardiogenic hotspots during heart morphogenesis and regeneration

(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
Series
Accession:
GSE172511
ID:
200172511
12.

Single-cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae

(Submitter supplied) Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single-cell RNA-sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin (cut) and intact caudal fine (uncut) samples were dissociated and loaded into the 10x Genomics Chromium Platform, and sequenced using Illumina NovaSeq 6000. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
2 Samples
Download data: MTX, TSV
Series
Accession:
GSE158851
ID:
200158851
13.

RNA-seq experiments on heart regeneration in WT, foxm1 and dusp6 mutants.

(Submitter supplied) The study compares gene expression profile at several stages post amputation of the adult zebrafish ventricular heart between zebrafish mutants and WT siblings. The first experiment was to identify genes that are activated in response to cardiac injury at 3 and 7 days post amputation (dpa). Dusp6 mutant hearts were reported to show an enhanced regenerative response. For this experiment, bulk RNA seq was obtained from WT and Dusp6 mutant hearts and genes increased at 3 and 7 dpa were identified. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18413
12 Samples
Download data: XLSX
Series
Accession:
GSE201139
ID:
200201139
14.

RNA sequencing analyses of grl/hey2-overexpressing hearts and control hearts, as well as grl/hey2-deficient hearts and wild-type hearts following ventricular resection at 7 dpa

(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
Series
Accession:
GSE129499
ID:
200129499
15.

AP-1 Regulates Chromatin Accessibility to Promote Sarcomere Disassembly and Cardiomyocyte Protrusion during Zebrafish Heart Regeneration

(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
Series
Accession:
GSE130940
ID:
200130940
16.

MicroRNA expression profiling of zebrafish heart regeneration

(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
Series
Accession:
GSE74494
ID:
200074494
17.

Prrx1b restricts fibrosis and promotes Nrg1-dependent cardiomyocyte proliferation during zebrafish heart regeneration

(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
Series
Accession:
GSE153170
ID:
200153170
18.

Multiple roles for Wwtr1 in cardiac wall maturation

(Submitter supplied) Cardiac trabeculation is a highly regulated process that starts with the delamination of cardiomyocytes from the compact wall to form stereotypical muscular ridges in the developing ventricle.  The Hippo signaling pathway has been implicated in cardiac development but many questions remain.  We investigated the role of Wwtr1, a nuclear effector of the Hippo pathway, in zebrafish and find that its loss results in hearts with reduced trabeculation. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20828
6 Samples
Download data: TXT
Series
Accession:
GSE103169
ID:
200103169
19.

siRNA knockdown of neonatal rat cardiac myocytes and fibroblasts

(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
Series
Accession:
GSE112464
ID:
200112464
20.

RNAseq of regenerating yap mutant zebrafish hearts

(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
Series
Accession:
GSE112452
ID:
200112452
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