Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Early gene expression of regenerating zebrafish hearts following water or atropine treatment

ABSTRACT: We report global RNA expression profiles from whole zebrafish hearts 24 hours after ventricle amputation. Zebrafish were exposed to atropine or water following surgery.

ORGANISM(S): Danio rerio

PROVIDER: GSE69775 | GEO | 2015/06/11

SECONDARY ACCESSION(S): PRJNA286744

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Early gene expression of regenerating zebrafish hearts following water or atropine treatment

Project description:We report global RNA expression profiles from whole zebrafish hearts 24 hours after ventricle amputation. Zebrafish were exposed to atropine or water following surgery. 15 zebrafish hearts were pooled per microarray chip. Amputated hearts of zebrafish exposed to atropine was compared to hearts of zebrafish exposed to water.

2015-06-11 | E-GEOD-69775 | biostudies-arrayexpress

scRNAseq of post-amputation regenerating zebrafish cardiac ventricle

Project description:scRNAseq of post-amputation regenerating zebrafish cardiac ventricle

| PRJEB52989 | ENA

RNA seq analysis of regenerating hearts from three models of successful cardiac regeneration

Project description:Defining conserved molecular pathways in animal models of successful cardiac regeneration could yield insight into why adult mammals have inadequate cardiac regeneration after injury. Here we describe a cross-species transcriptomic screen to identify evolutionarily conserved pathways in the early events of cardiac regeneration in three species that can regenerate myocardium after a major injury. In this study, we performed RNA-seq on regenerating hearts from three model organisms - axolotl, zebrafish and mouse. Apical resection was performed to amputate ~10 - 20% of the left ventricle in all three model organisms. Following resection, hearts were harvested at 12, 24 and 48 hours post-resection and subjected to RNA-seq. RNA-seq on sham controls (no ventricular amputation) was used as interanal control. This approach revealed upregulation of inflammatory genes in all three organisms during regeneration. Furthermore, upregulation of Complement 5a receptor1 (C5aR1) expression in the regenerating hearts of zebrafish, axolotls and mice was observed.

2018-02-01 | GSE108493 | GEO

Microarray analysis of 2,3,7,8-Tetrachlorodibenzo-p-dioxin Exposed Amputated Adult Zebrafish Heart Ventricles

Project description:The purpose of this experiment is to understand which transcripts are differentially expressed following exposure to TCDD. We used microarrays to understand global changes in gene signal intensity Adult zebrafish (danio rerio) were injected (i.p) to vehicle control or TCDD (70 ng/g) one day prior to heart ventricle amputation. A subset of fish were exposed but the hearts were not amputated. Amputated hearts were collected at 6 hours post amputation and 7 days post amputation and processed for microarray analysis

2011-11-29 | E-GEOD-33981 | biostudies-arrayexpress

scRNAseq of post-amputation regenerating zebrafish cardiac ventricle

Project description:Adult zebrafish hearts have the ability to regenerate. The roles of non-myocytes in this process have remained elusive. Here, we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 (E1) included interstitial cells obtained from uninjured, regenerating (3 days, 7 days and 14 days post-apical amputation). Experiment 2 (E2) included cells from uninjured, sham-operated (abdomen opened) and regenerating (3 days post-amputation) with and without MMP inhibitor (NSC40520) treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single, viable nucleated cells.

2022-03-01 | E-MTAB-10643 | biostudies-arrayexpress

Transcriptome analysis on wild type and mvp mutant zebrafish ventricles at 7dpa by Next Generation Sequencing

Project description:In contrast to mammals, the adult zebrafish hearts can regenerate within a short period. Upregulation of major vault protein (Mvp) expression after ventricle resection. To determine the impact of loss of mvp on transcriptome during heart regeneration, we pursued transcriptome analysis (RNA-Seq) on wild type and mvp mutant zebrafish hearts at 7 day-post-amputation.

2020-09-01 | GSE157170 | GEO

RNAseq of regenerating yap mutant zebrafish hearts

Project description:RNAseq of regenerating yap mutant zebrafish hearts

| PRJNA447594 | ENA

Disruption of immune responses hindered cardiac repair in zebrafish

Project description:We investigated the role and programming of early immune responses during zebrafish heart regeneration. We found zebrafish treated with anti-inflammatory steroid, beclomethasone, would suffer significantly reduction of its heart regenerative ability, leading to excessive collagen deposition in wound. Microarray approach was used to evaluate the differential expression of heart transcriptome between normal and impaired healing zebrafish, which provides an overall assessment of significant genes that were important for triggering regeneration in the hemostasis-inflammation phase. Three sets of samples each containing 10 zebrafish hearts were used: sham operation, DMSO-1dpa, beclomethasone-1dpa. (dpa= days post amputation) Objects were pre-exposed to water containing 0.25M-NM-<M beclomethasone or DMSO for 1 day. After ventricular resection surgery, objects were sacrificed with their ventricles harvested at the next day (i.e. 1dpa)

2013-06-24 | E-GEOD-41618 | biostudies-arrayexpress

Regenerating Zebrafish fins: Controls vs. regenerating fins (3 days following fin amputation)

Project description:Transcriptional profiling of zebrafish rergenerating fins comparing control fins and regenerating fins (3 days following fin amputation)

2017-02-09 | GSE58567 | GEO

Proteomic analysis of extracellular matrix remodeling during zebrafish heart regeneration

Project description:Adult zebrafish, in contrast to mammals, are able to regenerate their hearts in response to injury or experimental amputation. Our understanding of the cellular and molecular bases that underlie this process, although fragmentary, has increased significantly over the last years. However, the role of the extracellular matrix (ECM) during zebrafish heart regeneration has been comparatively rarely explored. Here, we set out to characterize the ECM protein composition in adult zebrafish hearts, and whether it changed during the regenerative response. For this purpose, we first established a decellularization protocol of adult zebrafish ventricles that significantly enriched the yield of ECM proteins. We then performed proteomic analyses of decellularized control hearts and at different times of regeneration. Our results show a dynamic change in ECM protein composition, most evident at the earliest (7 days post-amputation) time-point analyzed. Regeneration associated with sharp increases in specific ECM proteins, and with an overall decrease in collagens and cytoskeletal proteins. We finally tested by atomic force microscopy that the changes in ECM composition translated to decreased ECM stiffness. Our cumulative results identify changes in the protein composition and mechanical properties of the zebrafish heart ECM during regeneration.

2019-08-26 | PXD010092 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data