Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Wound healing process after ventricular resection in zebrafish: time course (zebrafish)

ABSTRACT: The mechanism of cardiomyocyte prliferation and migration after ventricular resection is a complex and dynamic process. To resolve this, we chose the zebrafish model organism for studying post-injury heart regeneration and wound healing progress via systems biology approach. Transcriptome microarray data and histological analysis of injured fish were sampled at different time points during recovery process. Time-course microarray data following wound healing of zebrafish were obatined. From this set of data, we constructed two intracellular protein–protein interaction (PPI) networks to provide insights into the ventricular resection wound healing mechanism.

ORGANISM(S): Danio rerio

PROVIDER: GSE72348 | GEO | 2018/04/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Wound healing process after TBI in zebrafish: time course (zebrafish)

2014-09-30 | GSE56375 | GEO

Wound healing process after TBI in zebrafish: time course (zebrafish)

Project description:The interaction between neurogenesis and angiogenesis after traumatic brain injury is a complex and dynamic process. To resolve this, we chose the zebrafish model organism for studying brain wound healing via systems biology approach. Transcriptome microarray data and histological analysis of injured fish were sampled at different time points during recovery process. Time-course microarray data following wound healing of zebrafish were obtained. From this set of data, we constructed two intracellular proteinM-bM-^@M-^Sprotein interaction (PPI) networks for the traumatic brain injury healing mechanism. Each fish in each group was injured by a 1.5 mm, 27G needle tip from day 0 to 28, respectively. These injured fish were collected at 0, 0.25, 1, 3, 6, 10, 15, 21, 28 dpi (day post injury). 0.625M-NM-<g of Cy3 cRNA for C. albicans array and 1.65 M-NM-<g of Cy3 cRNA for zebrafish array was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60M-BM-0C for 30 minutes. Each time point contain two biological repeats.

2014-09-30 | E-GEOD-56375 | biostudies-arrayexpress

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

Innate and adaptive immunity in zebrafish: time course (zebrafish)

2014-11-03 | GSE51603 | GEO

Innate and adaptive immunity in zebrafish: time course (zebrafish)

Project description:The interaction between fungal pathogen and host innnate and adaptive immunity during infection is a complex and dynamic process. To resolve this, we chose the zebrafish model organism as the host to study C. albicans infection via systems biology approach. Transcriptome microarray data and histological analysis of surviving fish were sampled at different post-infection time points. Time-course microarray data following primary and secondary infection of zebrafish by Candida albicans were obatined. From this set of data, we constructed two intracellular proteinM-bM-^@M-^Sprotein interaction (PPI) networks for primary and secondary responses of the host. Each fish in the first group was intraperitoneally injected with 1 M-CM-^W 10E5 and 1 M-CM-^W 10E7 CFU C. albicans at day 0 and 14, respectively. These infected fish were collected at 1, 2, 3, 6, 14, 17.5, 21 dpi (day post infection). For the second group, a second injection of C. albicans was given on 14th day of the first infeciton, and the repeated infeceted fish were collected at 2, 6, 12, 18, 24, 30, 36, 42 hours post second injection. 1.65 M-NM-<g of Cy3 cRNA for zebrafish array was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60M-BM-0C for 30 minutes. Each time points contain two biological repeats.

2014-11-03 | E-GEOD-51603 | biostudies-arrayexpress

Danio rerio

Project description:Wound healing process after TBI in zebrafish: time course (zebrafish)

| PRJNA243077 | ENA

Analysis of gene expression in zebrafish cornea during wound healing

Project description:The cornea, transparent and outermost structure of camera-type eyes, is prone to environmental challenges, but has remarkable wound healing capabilities which enables to preserve vision. The manner in which cell plasticity impacts wound healing remains to be determined. In this study, we report rapid wound closure after zebrafish corneal epithelium abrasion. Furthermore, by investigating the cellular and molecular events taking place during corneal epithelial closure, we show the induction of a bilateral response to a unilateral wound. Our transcriptomic results, together with our TGF-beta receptor inhibition experiments, demonstrate conclusively the crucial role of TGF-beta signaling in corneal wound healing. Finally, our results on Pax6 expression and bilateral wound healing, demonstrate the decisive impact of epithelial cell plasticity on the pace of healing. Altogether, our study describes terminally differentiated cell competencies in the healing of an injured cornea. These findings will enhance the translation of research on cell plasticity to organ regeneration.

2022-01-20 | GSE193784 | GEO

Timeseries of small RNA and mRNA expression during zebrafish heart regeneration

Project description:Adult zebrafish are capable of regenerating cardiac tissue following ventricular resection within 30 days. We profiled both small RNA and mRNA expression in uninjured (0dpa), 1, 3, 7, 14, 21 and 30 days post amputation to study biological processes orchestrate each stage of regeneration.

2018-05-29 | GSE106884 | GEO

Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β-catenin signaling at the early wound healing stage

Project description:Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing (RNA-Seq) is a high-throughput sequencing method facilitating quantification of gene expression in a precisely manner. Development of RNA-Seq technologies and their extensive data-analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. In this study, we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing (20 hour post lesion) and early proliferative (3 day post lesion) stages of regeneration. Moreover, we uncover Wnt/β-catenin signaling as a key pathway that is activated at the early wound healing stage.

2020-10-05 | E-MTAB-9321 | biostudies-arrayexpress

Disruption of immune responses hindered cardiac repair in zebrafish

2013-06-24 | GSE41618 | GEO

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