Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Development of a hepatic cryoinjury model to study liver regeneration

ABSTRACT: We developed a new model to study liver regeneration based on cryoinjury. Hepatic cryoinjury induced a localised necrotic and apoptotic lesion characterised by inflammation and infiltration of innate immune cells. Following this initial phase, we observed fibrosis, which resolved as regeneration re-established homeostasis in 30 days. Importantly, this approach enables the comparison of healthy and injured parenchyma with an individual animal, providing unique advantages to previous models. These datasets include Bulk RNA-seq of livers collected at sham, 1 dpci, 3 dpci, and 7 dpci.

ORGANISM(S): Danio rerio

PROVIDER: GSE245878 | GEO | 2023/11/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Metabolic reprogramming and membrane glycans remodelling drive zebrafish heart regeneration

Project description:label-free relative quantitation based on nLC-MS/MS performed on heart tissues in a clinically relevant zebrafish model of cardiac tissue regeneration . Each of the six samples (2dp Cl, 2dpS, 7dp Cl, 7dpS, 14dp Cl, 14dpS,) has been analysed in two technical replicates. dpci = days post cryoinjury; dps = days post sham

2022-11-14 | MSV000090703 | MassIVE

postnb lineage traced cells at 7 and 60 days post cryoinjury (dpi) during adult zebrafish cardiac ventricle regeneration

Project description:Contrary to mammals, zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast-like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP-GFP-loxP-mCherrycz1701 double transgenic line, we permanently label cells that expressed postnb at 3 and 4 days post injury (dpi) with mCherry by administration of 4-OHT. We sequenced mCherry-labelled cells obtained from the ventricular apex at 7 and 60 dpi.

2018-03-21 | GSE101199 | GEO

Single cell profiling of salamander heart under homeostasis and after cryoinjury.

Project description:Heart disease is the leading cause of mortality worldwide due to the limited regenerative capacity of the mammalian heart. Myocardial infarction causes massive cardiomyocyte apoptosis that is replaced by a fibrotic scar. In contrast to mammals, certain vertebrates such as fish and amphibians can regenerate cardiac muscle without scarring. Here, we established a cryoinjury model in the salamander species, Pleurodeles waltl. We performed single-cell RNA sequencing to profile the salamander heart and identified CLDN6 as a specific marker of epicardium, the outermost mesothelial layer enclosing the heart. Notably, lineage tracing experiments showed differentiation of CLDN6+ epicardium-derived cell intermediates into cardiomyocytes in response to injury. Additionally, scRNA-seq experiments suggested a differentiation trajectory that describes epicardial cell to myocyte conversion. Furthermore, ablation of these intermediates with Clostridium perfringens enterotoxin (CPE) blocked cardiac regeneration.

2022-02-21 | GSE180914 | GEO

Comparative transcriptional analysis on cardiac ventricles between cryoinjury and moderate physical exercise in zebrafish

Project description:We compared transcriptional changes between 1) Control vs. 96 hours post cardiac cryoinjury (hpci) and 2) Control vs. 96 hours post physical exercise.

2021-09-10 | GSE161641 | GEO

Role of IL33 on muscle regneration in aging

Project description:We compare the effect of IL-33 vs PBS on muscle regneration from 22-month old mice 8 days post-injury. These analyses from whole muscle provide insight into the role of IL-33 on regeneration in the context of aging. The tibialis anterior muscle from male C57BL/6 mice (22 months old) were cryo-injured using a liquid nitrogen chilled metal probe for 8 seconds. Mice received 2 ug of rIL-33 via intraparitoneal injection the day prior and the day following cryoinjury. 8 days post-injury whole muscle was harvested and snap frozen in liquid nitrogen. Whole muscle was then homogenized directly in TriZol and gene expression profiling was performed on Affymetrix Mouse Gene 1.0 ST Arrays.

2016-01-10 | E-GEOD-76695 | biostudies-arrayexpress

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

Project description: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. Using a cardiomyocyte-specific dominant-negative approach, we show that AP-1 promotes cardiomyocyte proliferation as well as chromatin accessibility at genes regulating sarcomere disassembly and cardiomyocyte protrusion into the injured area. We further find distinct temporal requirements for AP-1 during cardiac regeneration. Altogether, these results indicate that AP-1 plays a key role in the cardiomyocyte response to injury by promoting chromatin accessibility changes, allowing the activation of gene expression programs that support regeneration.

2020-06-10 | GSE130940 | GEO

GNPS - Metabolic reprogramming and membrane glycans remodelling drive zebrafish heart regeneration

2022-11-14 | MSV000090703 | GNPS

Differential gene expression in Danio rerio during optic nerve regeneration

2009-12-25 | GSE17854 | GEO

Differential gene expression in Danio rerio during optic nerve regeneration

Project description:To gain a better understanding of the factors necessary for successful CNS regeneration, a temporal analysis of the changes in gene expression in the eye caused by optic nerve injury was conducted. Dual color oligonucleotide microarrays were used to compare total RNA harvested from the eyes of sham-operated and optic nerve-injured fish at 3, 24, and 168 hours following surgery. Optic nerve injured fish are compared to sham-operated fish in order to eliminate gene expression due to non-neuronal damage and inflammatory response. Statistical analyses identified 131 genes with a 2.0-fold or greater difference in expression. Wild type zebrafish were obtained from a local pet store. Optic nerve injury was conducted using a severing model accomplished as follows. Zebrafish were anesthetized in 0.2% MS-222 dissolved in tank water. The muscles surrounding the eye were cut and the eye angled rostrally to expose the nerve. The optic nerve was then severed using microsissors without damaging the ophthalmic artery. In sham operated fish the muscles surrounding the eye were severed but the nerve was not damaged. RNA was extracted from the eye at three time points following surgery 3 hours, 24 hours, and 168 hours. RNA was pooled from multiple fish to achieve 10 ug total RNA. Samples were collected in triplicate per time point. Gene expression was analyzed on a dual color oligonucleotide array where the optic nerve injured fish were compared to sham-operated fish. Four samples of RNA were also collected from control fish and compared to each other on the microarray to confirm that processing did not create expression differences.

2010-05-16 | E-GEOD-17854 | biostudies-arrayexpress

Telomerase is essential for zebrafish heart regeneration

Project description: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. Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq, in control conditions and 3 days after heart cryoinjury.

2015-08-06 | E-GEOD-71755 | biostudies-arrayexpress

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