Timeseries of small RNA and mRNA expression during zebrafish heart regeneration
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE106884 | GEO | 2018/05/29
REPOSITORIES: GEO
Similar Datasets
Project description:We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins
2016-04-08 | GSE76564 | GEO
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
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
Project description:The salamander microRNA expression between mid-bud limb regenerating blastemas (17 days post amputation) and non-regenerating stump tissues was compared by microarray analysis.
2012-11-06 | GSE29727 | GEO
Project description:The study compares gene expression profile at 20 days post amputation of the zebrafish ventricular heart between dusp6 mutant and WT siblings.
2018-02-18 | GSE90595 | GEO
Project description:The adult vertebrate red spotted newt is a champion of regeneration, demonstrating an amazing ability to regenerate damaged organs and tissues back to an uninjured state without the formation of scar or reduction in function. By developing a novel cardiac resection strategy, our group recently demonstrated that newt hearts could morphologically and functionally regenerate, without scarring, within a period of 2-3 months following injury. MicroRNAs (miRs) have been widely publicized as essential post-transcriptional gene regulators in a variety of biological processes, including regeneration. We have conducted a microarray screen for vertebrate miRs, with several candidate miRs showing significant differential expression at important time-points following injury to the newt heart. The newt microRNA expression between uninjured hearts and regenerating hearts, 7 and 21 days post-injury (dpi), was compared by microarray analysis. Three paired samples were analyzed: Uninjured, 7dpi and 21dpi newt hearts. Three arrays were hybridized comparing two-paired samples each time.
2013-09-24 | E-GEOD-44547 | biostudies-arrayexpress
Project description:We used Nimblegen arrays with design 2007-11-06_Smed_ESTs_4_exp to measure changes in gene expression during a timecourse of regeneration of one side of the head in Schmidtea mediterranea flatworms. Following amputation of one side of the head, samples were collected from both the regeneration blastema and non-regenerating side of the head on days 2, 3, and 4 post-amputation. Gene expression in these samples was compared to that in non-regenerating control samples collected at the time of amputation.
2014-12-01 | GSE62551 | GEO
Project description:Mice were subjected to hindlimb distal phalanx (P3) amputation to digit 3. For each amputation, mice were anesthetized, the hindlimb claw was extended, and the distal phalanx and footpad was sharply dissected. A regenerating distal phalanx was generated by amputating ≤33% of the P3. Skin wounds were allowed to heal without suturing. Mice were subjected to micro-computed tomography (microCT) one day prior to surgery and immediately after amputation to confirm ≤ 33% removal of the P3. Any digit that did not fall within the ≤ 33% amputation guideline was omitted from the study. Based on our criteria, 17 animals were removed from the study resulting in a final total of 30 mice. P3 mice were collected at hours (0h, 3h, 6h ,12h, and 24h), and days (3d, 7d, 14d, and 21d). Each time point contained 3 mice, except day 7 (6 mice). At the time of P3 collection, samples were immediately immersed in RNAlater for 24h at 4C. The digits were then removed from RNAlater and stored at -80C until performing RNA sequencing.
2020-02-19 | GSE130438 | GEO
Project description:The adult vertebrate red spotted newt is a champion of regeneration, demonstrating an amazing ability to regenerate damaged organs and tissues back to an uninjured state without the formation of scar or reduction in function. By developing a novel cardiac resection strategy, our group recently demonstrated that newt hearts could morphologically and functionally regenerate, without scarring, within a period of 2-3 months following injury. MicroRNAs (miRs) have been widely publicized as essential post-transcriptional gene regulators in a variety of biological processes, including regeneration. We have conducted a microarray screen for vertebrate miRs, with several candidate miRs showing significant differential expression at important time-points following injury to the newt heart. The newt microRNA expression between uninjured hearts and regenerating hearts, 7 and 21 days post-injury (dpi), was compared by microarray analysis.
2013-09-24 | GSE44547 | GEO
Project description:Xenopus laevis tadpoles are capable of limb regeneration following amputation, in a process which initially involves the formation of a blastema. However, Xenopus has full regenerative capacity only through premetamorphic stages. We have used the Affymetrix Xenopus laevis Genome Genechip® microarray to perform a large-scale screen of gene expression in the regeneration-complete, stage 53 (st53), and regeneration-incomplete, stage 57 (st57), hindlimbs at 1 and 5 days post-amputation. Through an exhaustive reannotation of the Genechip® and a variety of comparative bioinformatic analyses, we have identified genes that are differentially expressed between the regeneration-complete and âincomplete stages, detected the transcriptional changes associated with the regenerating blastema, and compared these results with those of other regeneration researchers. We focus particular attention on striking transcriptional activity observed in genes associated with patterning, stress response, and inflammation. Overall, this work provides the most comprehensive views yet of a regenerating limb and different transcriptional compositions of regeneration-competent and deficient tissues. Experiment Overall Design: This experiment measures gene expression in regeneration competent stage 53 and regeneration non-competent stage 57 Xenopus laevis hindlimbs, at 1 and 5 days post-amputation. Four replicates for each condition were used. Hindlimbs at either st53 or st57 were amputated unilaterally or bilaterally at the mid-zeugopodia level. One (1dPA) and 5 days (5dPA) after amputation tissues were collected 1mm proximal to the original level of amputation. Total RNA was isolated using RNaqueous micro kit (Ambion, inc.). One microgram of total RNA was amplified with the the Affymetrix 2 cycle kit and assayed per Genechip using standard Affymetrix protocols.
2008-06-13 | E-GEOD-4738 | biostudies-arrayexpress