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.
Project description:Transcriptional profiling of zebrafish rergenerating fins comparing control fins and regenerating fins (3 days following fin amputation)
Project description:Transcriptional profiling of zebrafish rergenerating fins comparing normoxic renenerating fins and hypoxic regenerating fins (3 days following fin amputation)
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.
Project description:Adult zebrafish can completely regenerate their caudal fin following amputation. This complex process is initiated by the formation of an epithelial would cap over the amputation site by 12 hours post amputation (hpa). Once the cap is formed, mesenchymal cells proliferate and migrate from sites distal to the wound plane and accumulate under the epithelial cap forming the blastemal structure within 48 hpa. Blastemal cells proliferate and differentiate, replacing the amputated tissues, which are populated with angiogenic vessels and innervating nerves during the regenerative outgrowth phase which is completed around 14 days post amputation (dpa). Regenerative outgrowth does not occur in TCDD-exposed zebrafish. To identify the molecular pathways that are perturbed by TCDD exposure, male zebrafish were i.p. injected with 50 ng/g TCDD or vehicle and caudal fins were amputated. Regenerating fin tissue was collected at 1, 3 and 5 dpa for mRNA abundance analysis. Microarray analysis and quantitative real time PCR revealed that wound healing and regeneration alone altered the expression of nearly 900 genes by at least two fold between 1 and 5 dpa. TCDD altered the abundance of 370 genes at least two fold. Among these, several known aryl hydrocarbon responsive genes were identified in addition to several genes involved in extracellular matrix composition and metabolism. The profile of misexpressed genes is suggestive of impaired cellular differentiation and extracellular matrix composition potentially regulated by Sox9b. Keywords: Time course and TCDD exposure response
Project description:Expression of genes encoding multiple keratin- and keratin-associated proteins varies between C57BL/6 and MRL/MpJ (superhealer) mice following digit amputation. We characterized changes in gene expression by microarray analysis of regenerating digits in these mice at various timepoints following surgical amputation. These changes were validated by quantitative rtPCR analyses. In this dataset, we include the expression data obtained from regenerating mouse digits following surgical amputation as well unamputated digits (total 24 samples). These data are used to obtain genes that are differentially expressed between the two groups of digits.
Project description:Treatment with midkine inhibitor iMDK inhibits limb regeneration. To elucidate the transcriptional mechanisms of iMDK treatment, we sequenced regenerating limbs treated with either DMSO or iMDK (bulk) in biological triplicate at 11 days post-amputation (dpa).
Project description:Zebrafish caudal fin regeneration is an established model to study tissue regeneration. In order to identify novel molecular signaling pathways critical for regeneration, we developed a rapid throughput in vivo regeneration assay. We screened a 2000 member structurally diverse small molecule library, followed by assessment of regenerative progression at three days post amputation. A cluster of glucocorticoids was identified among the âpositive hitsâ. To identify the molecular targets of the activated glucocorticoid receptor, microarray analysis was performed using RNA isolated from the regenerates of control and glucocorticoid exposed zebrafish. We identified 673 transcripts that were differentially regulated. The level of expression and spatial expression pattern of select genes were completed by qPCR and by in situ hybridization, respectively. Altogether, these studies demonstrate the power of chemical genetics to identify chemical probes and their targets which will provide a path towards defining conserved regenerative pathways. Experiment Overall Design: The caudal fin of zebrafish larvae at 2days post fertilization were amputated and exposed to vehicle control alone or Beclomethasone . Regenerating fins were isolated at 1days post amputation. Three replicates were collected at each time point. 150 fins were pooled to comprise one replicate.
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.
Project description:Here we present single-cell RNA sequencing (scRNA-seq) data of untreated digit amputation wound cells that can be induced by BMP9 to undergo chondrogenesis to determine the responsive cell type