Project description:Zebrafish have been found to be a premier model organism in biological and regeneration research. However, the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here, we utilized Microwell-seq to analyze more than 250,000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single-cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single-cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall, our single-cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research.
Project description:We applied single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) to determine the intrinsic genetic programs underlying nonCM subpopulation determination during zebrafish heart regeneration at a single cell level. A total of approximately 13,000 single non-CMs derived from zebrafish hearts isolated at different time points during heart regeneration were measured and defined into diverse cell populations, exploited for cell type-specific cis-regulatory elements and enriched motifs as control catalog of downstream cell-state-determining transcription factors.
Project description:We applied single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) to determine the intrinsic genetic programs underlying nonCM subpopulation determination during zebrafish heart regeneration at a single cell level. A total of approximately 13,000 single non-CMs derived from zebrafish hearts isolated at different time points during heart regeneration were measured and defined into diverse cell populations, exploited for cell type-specific cis-regulatory elements and enriched motifs as control catalog of downstream cell-state-determining transcription factors.
Project description:Using adult zebrafish inner ears as a model for sensorineural regeneration, we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single-cell epigenome and transcriptome at consecutive time-points following hair cell death.
Project description:Using single-cell RNA sequencing, we pictured a dynamic landscape of the intestinal microenvironment during RIII and regeneration. We generated transcriptomes of 22,680 single cells in the intestinal microenvironment, trying to profile the dynamics of ISCs and immune cells located in the mucous layer. This large-scale single-cell transcriptome data can be used as a valuable resource for further studying the cellular mechanism of RIII and development of potential therapy strategies.
Project description:By contrast with mammals, adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of spared cardiomyocytes. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source, and has received recent attention as a target in cardiac repair strategies. While it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential, the extent of cellular heterogeneity within epicardial tissue is largely unexplored. In this study, we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan-epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan-epicardial and epicardial markers by alternative expression assays. Additionally, we explored the function of the scaffolding protein and main component of caveolae, caveolin-1 (cav1), which was present in each epicardial subset. In BAC transgenic zebrafish, cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover, cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy, but displayed profound defects in injury-induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers, genetic tools, and mechanisms of heart regeneration. Deep sequencing of isolated single epicardial cells
Project description:We applied single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) to determine the intrinsic genetic programs underlying nonCM subpopulation determination during zebrafish heart regeneration at a single cell level. A total of approximately 13,000 single non-CMs derived from zebrafish hearts isolated at different time points during heart regeneration were measured and defined into diverse cell populations, exploited for cell type-specific cis-regulatory elements and enriched motifs as control catalog of downstream cell-state-determining transcription factors.
