PROJECT ID: PRJNA706197

Data source SRA: PRJNA706197
Description We have performed single-cell RNA-seq of cranial NC cells in zebrafish over several stages during their migration
Key word fate decisions; foxd3 activity; twist; differentiation; restrictions; expression; migration; melanocytes; genes; trunk
Publication Tatarakis D, Cang Z, Wu X, Sharma PP et al. Single-cell transcriptomic analysis of zebrafish cranial neural crest reveals spatiotemporal regulation of lineage decisions during development. Cell Rep 2021 Dec 21;37(12):110140. PMID: 34936864
Abstract Neural crest (NC) cells migrate throughout vertebrate embryos to give rise to a huge variety of cell types, but when and where lineages emerge and their regulation remain unclear. We have performed single-cell RNA sequencing (RNA-seq) of cranial NC cells from the first pharyngeal arch in zebrafish over several stages during migration. Computational analysis combining pseudotime and real-time data reveals that these NC cells first adopt a transitional state, becoming specified mid-migration, with the first lineage decisions being skeletal and pigment, followed by neural and glial progenitors. In addition, by computationally integrating these data with RNA-seq data from a transgenic Wnt reporter line, we identify gene cohorts with similar temporal responses to Wnts during migration and show that one, Atp6ap2, is required for melanocyte differentiation. Together, our results show that cranial NC cell lineages arise progressively and uncover a series of spatially restricted cell interactions likely to regulate such cell-fate decisions.


Dataset Information

Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. PRJNA706197 (12hpf) Danio rerio embryo baseline 12hpf, FACS sorted sox10:nEOS cells SRA: SRR13839954
2. PRJNA706197 (14hpf) Danio rerio embryo baseline 14hpf, FACS sorted sox10:nEOS cells SRA: SRR13839958
3. PRJNA706197 (20hpf) Danio rerio embryo baseline 20hpf, FACS sorted sox10:nEOS cells SRA: SRR13839965
4. PRJNA706197 (24hpf) Danio rerio embryo baseline 24hpf, FACS sorted sox10:nEOS cells SRA: SRR13839972
5. PRJNA706197 (1.25dpf) Danio rerio embryo baseline 1.25dpf, FACS sorted sox10:nEOS cells SRA: SRR13839973
6. PRJNA706197 (18hpf) Danio rerio embryo baseline 18hpf, FACS sorted sox10:nEOS cells SRA: SRR13839979

Clustering Result

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Neural crest ENSDARG00000077467 (sox10) marker DOI:10.1016/j.celrep.2021.110140
2 Neural crest ENSDARG00000077467 (sox10) marker DOI:10.1016/j.celrep.2021.110140

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Neural crest ENSDARG00000077467 (sox10) marker DOI:10.1016/j.celrep.2021.110140

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Neural crest ENSDARG00000030402 (twist1a) marker DOI:10.1016/j.celrep.2021.110140
2 Neural tube ENSDARG00000010770 (sox19a) marker DOI:10.1016/j.celrep.2021.110140
3 Neural crest ENSDARG00000077467 (sox10) marker DOI:10.1016/j.celrep.2021.110140
4 Epithelial cells ENSDARG00000040534 (epcam) marker DOI:10.1016/j.celrep.2021.110140
4 Epithelial cells ENSDARG00000017624 (krt4) marker DOI:10.1016/j.celrep.2021.110140
5 Endothelium ENSDARG00000000767 (spi1b) marker DOI:10.1016/j.celrep.2021.110140

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Neural crest ENSDARG00000030402 (twist1a) marker DOI:10.1016/j.celrep.2021.110140
2 Epithelial cells ENSDARG00000040534 (epcam) marker DOI:10.1016/j.celrep.2021.110140
2 Epithelial cells ENSDARG00000017624 (krt4) marker DOI:10.1016/j.celrep.2021.110140
3 Neural crest ENSDARG00000008861 (tfap2e) marker DOI:10.1016/j.celrep.2021.110140

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Neural crest ENSDARG00000030402 (twist1a) marker DOI:10.1016/j.celrep.2021.110140
2 Neural crest ENSDARG00000030402 (twist1a) marker DOI:10.1016/j.celrep.2021.110140
3 Epithelial cells ENSDARG00000040534 (epcam) marker DOI:10.1016/j.celrep.2021.110140

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Neural crest ENSDARG00000030402 (twist1a) marker DOI:10.1016/j.celrep.2021.110140
2 Epithelial cells ENSDARG00000040534 (epcam) marker DOI:10.1016/j.celrep.2021.110140
3 Endothelium ENSDARG00000000767 (spi1b) marker DOI:10.1016/j.celrep.2021.110140
4 Neural crest ENSDARG00000008861 (tfap2e) marker DOI:10.1016/j.celrep.2021.110140
5 Cardiac mesoderm ENSDARG00000032976 (cmlc1) marker DOI:10.1016/j.celrep.2021.110140
5 Cardiac mesoderm ENSDARG00000076126 (actc1a) marker DOI:10.1016/j.celrep.2021.110140
6 Endothelium ENSDARG00000105215 (kdrl) marker DOI:10.1016/j.celrep.2021.110140
7 Epithelial cells ENSDARG00000017624 (krt4) marker DOI:10.1016/j.celrep.2021.110140
8 Fibroblasts ENSDARG00000036869 (tcf21) marker DOI:10.1016/j.celrep.2021.110140