Data source GEO: GSE163907
Description Single cell RNA-seq data of tg(sox10:GFP) cells from 20-24 hours post fertilization zebrafish. Sequenced with 10x genomics.
Key word reveals multipotency; zebrafish; trunk; specification; fate; restrictions; evolution; pattern; prdm1a
Publication Lencer E, Prekeris R, Artinger KB. Single-cell RNA analysis identifies pre-migratory neural crest cells expressing markers of differentiated derivatives. Elife 2021 Aug 16;10. PMID: 34397384
Abstract The neural crest is a migratory population of stem-like cells that contribute to multiple traits including the bones of the skull, peripheral nervous system, and pigment. How neural crest cells differentiate into diverse cell types is a fundamental question in the study of vertebrate biology. Here, we use single-cell RNA sequencing to characterize transcriptional changes associated with neural crest cell development in the zebrafish trunk during the early stages of migration. We show that neural crest cells are transcriptionally diverse and identify pre-migratory populations already expressing genes associated with differentiated derivatives, specifically in the xanthophore lineage. Further, we identify a population of Rohon–Beard neurons in the data. The data presented identify novel genetic markers for multiple trunk neural crest cell populations and Rohon–Beard neurons providing insight into previously uncharacterized genes critical for vertebrate development.

Dataset Information

Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. GSE163907 (24hpf) Danio rerio trunk baseline 24hpf, trunk tg(sox10:GFP) positive cells GEO: GSM4990514

Clustering Result

Cluster Cell type Gene id (symbol) Marker class Evidence
1 TNCC progenitors ENSDARG00000053959 (cdc42ep2) marker DOI:10.7554/eLife.66078
2 Posterior arch ENSDARG00000079964 (dlx2a) marker DOI:10.7554/eLife.66078
3 Xanthoblast ENSDARG00000071475 (aox5) marker DOI:10.7554/eLife.66078
4 Pigment cells ENSDARG00000003732 (mitfa) marker DOI:10.7554/eLife.66078
7 Otic ENSDARG00000040534 (epcam) marker DOI:10.7554/eLife.66078
9 Mesenchymal cells ENSDARG00000100133 (cnmd) marker DOI:10.7554/eLife.66078