Similar Datasets
Project description: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. Altered expression of all genes was confirmed with qRT–PCR. Conclusions: Our study represents the detailed analysis of 4 dpci wild-type and ccn2a-/- cardiac ventricular transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that 7 genes were dysregulated in 4 dpci ccn2a-/- cardiac ventricle. We concluded, this analysis helped us to identify downstream signalling cascade of Ccn2a in injured zebrafish heart."
2021-01-12 | GSE164491 | GEO
Project description:Previous studies have suggested that the heart may be capable of limited repair and regeneration in response to a focal injury while other studies indicate that the mammalian heart has no regenerative capacity. To further explore this issue, we performed a series of superficial and transmural myocardial injuries in C57BL/6 and MRL/MpJ adult mice. At defined time intervals following the respective injury (Days 3, 14, 30 and 60) we examined cardiac function using echocardiography, morphology, FACS cell sorting for BrdU positive cells and molecular signature using microarray analysis. We observed complete restoration of myocardial function in the superficial MRL cryoinjured heart and significantly less scar formation as compared to the injured hearts of C57BL/6 mice. Following a severe transmural myocardial injury, the MRL mouse has increased survival and decreased ventricular remodeling compared to the C57BL/6 mouse but without evidence of significant regeneration. The cytoprotective program observed in the severely injured MRL heart is in part due to increased vasculogenesis and decreased apoptosis that limits the extension of the injury. We conclude that C57BL/6 and MRL injured hearts have evidence of limited myocardial regeneration, in response to superficial injury, but the improved function and survival observed in the MRL mouse heart following severe injury is not due to significant regenerative processes. Mouse hearts from C57BL/6 and MRL/MpJ strains were injured with LAD ligation and harvested at 3, 30 and 60 days after treatement.
2007-11-23 | E-GEOD-4710 | biostudies-arrayexpress
Project description:After heart injury, adult zebrafish can perfectly regenerate its heart without any scar tissue left. We performed 100bp*2, paired-end, strand-specific, polyA-positive RNA-seq on hearts from 2 group of adult zebrafish, in which one was sham group and the other 7 days after heart tip amputation (7dpa). We found pathways involving hydrogen peroxidate related functions significantly up-regulated in 7dpa group, indicating its role in heart regeneration. RNA-seq: hearts from sham or 7dpa adult zebrafish
2014-12-24 | E-GEOD-50203 | biostudies-arrayexpress
Project description:The study was designed to identify genes regulated after spinal transection that might contribute to regenerative growth of neurons projecting from the NMLF in Zebrafish. Zebrafish were injured by surgical transection of the spinal cord at 1 mm caudal to the brainstem-spinal cord junction (Injured). Animals receiving sham surgery (identical surgical procedures without transection) served as control (Control). The nucleus of the medial longitudinal fascicle (NMLF) was laser capture microdissected from approximately 30 frozen sections. RNA was prepared, amplified, and run on Affymetrix Zebrafish arrays.
2011-12-01 | GSE28470 | GEO
Project description:Analysis of the roles of Irx3 and Irx5 transcription factors in mouse heart development and postnatal heart function. Results show that show that Irx3 and Irx5 have redundant function in the in the endocardium to regulate atrioventricular canal morphogenesis and outflow tract formation. A postnatal deletion of Irx3 and Irx5 surprisingly results in a restoration of the repolarization gradient that is altered in Irx5 mutant hearts, suggesting a model whereby postnatal Irx3 activity is normally repressed by Irx5. 4 genotypes were analyzed: Irx5+/- (3 samples), Irx3-/-;Irx5+/- (4 samples), Irx5-/- (3 samples), Irx5-/-;Irx3-/- (4 samples). The Irx5+/- samples are the reference.
2012-06-19 | E-GEOD-38826 | biostudies-arrayexpress
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
Project description:Platelet-derived growth factor (PDGF) signaling regulates perivascular cell or mural cell association with the blood-vessel endothelial cells. Mural cells express the receptor of the signaling, pdgfrb. Besides mural cells the outer epithelial layer of the heart, epicardium and epicardial derived cells express pdgfrb. In this dataset we characterized pdgfrb expressing cells in adult zebrafish heart ventricles in AB wildtype fish, pdgfrb loss-of-function mutant fish. Since pdgfrb is activated in injured zebrafish heart, we aslo compared pdgfrb expressing cells in injured (amputated, 7 days post amputation) heart ventricle with similar cells in uninjured hearts.
2022-02-19 | GSE188511 | GEO
Project description:The zebrafish has the capacity to regenerate its heart after severe injury. While the function of a few genes during this process has been studied, we are far from fully understanding how genes interact to coordinate heart regeneration. To enable systematic insights into this phenomenon, we generated and integrated a dynamic co-expression network of heart regeneration in the zebrafish and linked systems-level properties to the underlying molecular events. Across multiple post-injury time points, the network displays topological attributes of biological relevance. We show that regeneration steps are mediated by modules of transcriptionally coordinated genes, and by genes acting as network hubs. We also established direct associations between hubs and validated drivers of heart regeneration with murine and human orthologs. The resulting models and interactive analysis tools are available at http://infused.vital-it.ch. Using a worked example, we demonstrate the usefulness of this unique open resource for hypothesis generation and in silico screening for genes involved in heart regeneration. In order to monitor the whole regeneration process, we recovered samples at different time points post-injury: 4 h, 1 day, 3 days, 7 days, 14 days and 90 days (respectively 4 hpi, 1 dpi, 3 dpi, 7 dpi, 14 dpi and 90 dpi). Cryoinjured hearts were compared to healthy hearts from control fish in 3 independent experiments.
2016-06-01 | E-GEOD-67665 | biostudies-arrayexpress
Project description:The study was designed to identify genes regulated after spinal transection that might contribute to regenerative growth of neurons projecting from the NMLF in Zebrafish. Zebrafish were injured by surgical transection of the spinal cord at 1 mm caudal to the brainstem-spinal cord junction (Injured). Animals receiving sham surgery (identical surgical procedures without transection) served as control (Control). The nucleus of the medial longitudinal fascicle (NMLF) was laser capture microdissected from approximately 30 frozen sections. RNA was prepared, amplified, and run on Affymetrix Zebrafish arrays. Zebrafish were used because they recover swimming function after spinal transection in about 6 weeks. The NMLF has been identified as a prominent group of neurons that descend through the site of injury in the spinal cord and that regenerate after injury. Times were selected to distinguish early events from those in the timeframe of regenerative growth.
2011-12-01 | E-GEOD-28470 | biostudies-arrayexpress
Project description:Transcriptome sequencing of SIS3-treated uninjured (5dpf) and injured (2dpt) zebrafish hearts.
2021-04-07 | GSE162820 | GEO