GSM6133973: epicardial cells, scRNA-seq; Danio rerio; RNA-Seq - SRA

SRX15241415: GSM6133973: epicardial cells, scRNA-seq; Danio rerio; RNA-Seq
2 ILLUMINA (Illumina HiSeq 4000) runs: 68M spots, 9.1G bases, 4.6Gb downloads

External Id: GSM6133973_r1

Submitted by: Applied Bioinformatics Core, Physiology & Biophysics, Weill Cornell Medicine

Study: An injury-associated transient progenitor state in the epicardium mediates heart regeneration

PRJNA837476 • SRP374910 • All experiments • All runs

show Abstracthide Abstract

Adult zebrafish regenerate heart muscle after severe cardiac damage without significant scarring. The epicardium, a mesothelial cell sheet covering the vetebrate heart, is activated by injury and supports muscle regeneration through paracrine effects and as a source of multipotent cells. The understudied cellular heterogeneity of the adult epicardium during heart regeneration has constrained the effort in mobilizing the epicardium for heart repair. To dissect epicardial cell states and the underlying mechanisms that lead to successful heart regeneration in zebrafish, we performed single-cell RNA-sequencing of isolated epicardial cells from the regenerating adult heart and revealed their dynamic cellular heterogeneity. We defined the epithelial and mesenchymal layers of the epicardium and identified a transiently activated epicardial progenitor cell (aEPC) subpopulation that expresses aldh1a2, ptx3a, col12a1b and marcksb. Upon heart amputation injury, aEPCs emerge from the existing epicardial cells, migrate to enclose the wound, and disappear as regeneration progresses. Genetic lineage tracing combined with modified RNA labelling confirmed an epithelial-mesenchymal transition (EMT) process of aEPCs and their differentiations to pdgfrb+ mural cells and pdgfra+hapln1a+ mesenchymal fibroblast-like cells that support heart regeneration. Genetic ablation of aEPCs blocked wound closure of the injured ventricle, suppressed cardiomyocyte proliferation, and disrupted heart regeneration. Our findings define a transient progenitor state of the adult epicardium that is an indispensable driver of zebrafish heart regeneration and identified ptx3a as a regeneration-specific non-ontogenetic regulator of the epicardium. Overall design: Single-cell RNA sequencing of isolated epicardial cells from uninjured zebrafish hearts and hearts after amputation injury

Sample: epicardial cells, scRNA-seq

SAMN28204117 • SRS12974374 • All experiments • All runs

Organism: Danio rerio

Library:

Name: GSM6133973

Instrument: Illumina HiSeq 4000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC SINGLE CELL

Selection: cDNA

Layout: PAIRED

Construction protocol: Hearts were dissociated into single cells and the epicardial cells were isolated by FACS as described previously (PMID 26657776). Library prep was performed according to the manufacturer's instructions (single cell 3' v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with, amplified by PCR and the appropriate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Single Cell 3' GEM (Gel Bead Kit v3, Chromium Single Cell B Chip Kit)

Runs: 2 runs, 68M spots, 9.1G bases, 4.6Gb

Run	# of Spots	# of Bases	Size	Published
SRR19176074	34,577,391	4.6G	2.4Gb	2022-11-22
SRR19176075	33,435,549	4.5G	2.3Gb	2022-11-22

ID:: 21719996

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