Gene expression profile at single cell level of sclerotome-derived fibroblasts from 52 hours post fertilization (hpf) transgenic zebrafish trunks.

The sclerotome region of the somite (labelled by nkx3.1:Gal4-VP16; UAS:NTR-mCherry) gives rise to numerous fibroblasts populations in the zebrafish trunk. We performed single cell RNA sequencing (scRNA-seq) on sclerotome-derived fibroblasts from 52 hpf embryos to determine population heterogeneity and plasticity. scRNA-seq was performed on mCherry-positive cells from trunk regions of 52 hpf Tg BAC(nkx3.1:Gal4-VP16)ca101; Tg(UAS:NTR-mCherry)ca264 zebrafish isolated by Fluorescence-activated cell sorting (FACS). The single cell library was prepared using 10X Genomics 3’ gene expression profiling droplet-based scRNA-seq technology (v3.1 chemistry) according to manufacturer’s protocols. Sequencing was performed on the using the Illumina NovaSeq S2 flow cell.