PROJECT ID: PRJNA640816


Data source SRA: PRJNA640816
Description Neural crest cells (NCCs) are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here, we utilized single-cell transcriptomic analyses to delineate NCC-derivatives along the posterior developing vertebrate, zebrafish, during the late embryonic to early larval stage, a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC-derived cell-types including mesenchyme, neural crest, neural, neuronal, glial, and pigment, from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages, mesenchyme subtypes, and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes, with distinct profiles within neuronal cells. From these analyses, we present a comprehensive cell-type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation.
Key word enteric nervous-system; nitric-oxide synthase; gene-expression; hox-genes; migration; roles; vagal; evolution; image; mouse
Publication Howard AG 4th, Baker PA, Ibarra-García-Padilla R, Moore JA et al. An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution. Elife 2021 Feb 16;10. PMID: 33591267
Abstract Neural crest cells (NCCs) are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here, we utilized single-cell transcriptomic analyses to delineate NCC-derivatives along the posterior developing vertebrate, zebrafish, during the late embryonic to early larval stage, a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC-derived cell-types including mesenchyme, neural crest, neural, neuronal, glial, and pigment, from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages, mesenchyme cells, and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes, with distinct profiles within neuronal cells. From these analyses, we present a comprehensive cell-type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation.


Dataset Information


Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. PRJNA640816 (2dpf) Danio rerio embryo baseline 2dpf, FACS isolated -4.9sox10:EGFP+ cells SRA: SRR12060552
2. PRJNA640816 (2.9dpf) Danio rerio embryo baseline 2.9dpf, FACS isolated -4.9sox10:EGFP+ cells SRA: SRR12060555

Clustering Result


Cluster Cell type Gene id (symbol) Marker class Evidence
1 Melanoma cells ENSDARG00000054155 (pcna) marker DOI:10.7554/eLife.60005
3 Neuron ENSDARG00000033655 (stmn1b) marker DOI:10.7554/eLife.60005
3 Neuron ENSDARG00000014420 (elavl3) marker DOI:10.7554/eLife.60005
3 Neuron ENSDARG00000045639 (elavl4) marker DOI:10.7554/eLife.60005
4 Melanoma cells ENSDARG00000020007 (col1a2) marker DOI:10.7554/eLife.60005
5 Melanoma cells ENSDARG00000058730 (rdh10a) marker DOI:10.7554/eLife.60005
6 Neural crest ENSDARG00000021032 (foxd3) marker DOI:10.7554/eLife.60005
6 Neural crest ENSDARG00000089223 (ngfrb) marker DOI:10.7554/eLife.60005
7 Pigment cells ENSDARG00000006008 (dct) marker DOI:10.7554/eLife.60005
7 Pigment cells ENSDARG00000003732 (mitfa) marker DOI:10.7554/eLife.60005
7 Pigment cells ENSDARG00000056151 (tyrp1b) marker DOI:10.7554/eLife.60005
7 Pigment cells ENSDARG00000029204 (tyrp1a) marker DOI:10.7554/eLife.60005
9 Glia ENSDARG00000025301 (gfap) marker DOI:10.7554/eLife.60005
10 Otic ENSDARG00000009544 (cldnb) marker DOI:10.7554/eLife.60005
11 Muscle cells ENSDARG00000070835 (tnnc2) marker DOI:10.7554/eLife.60005

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Melanoma cells ENSDARG00000020007 (col1a2) marker DOI:10.7554/eLife.60005
1 Melanoma cells ENSDARG00000012593 (col5a1) marker DOI:10.7554/eLife.60005
2 Melanoma cells ENSDARG00000069093 (col2a1a) marker DOI:10.7554/eLife.60005
3 Neural crest ENSDARG00000021032 (foxd3) marker DOI:10.7554/eLife.60005
4 Muscle cells ENSDARG00000033683 (tpma) marker DOI:10.7554/eLife.60005
4 Muscle cells ENSDARG00000099197 (actc1b) marker DOI:10.7554/eLife.60005
5 Pigment cells ENSDARG00000029204 (tyrp1a) marker DOI:10.7554/eLife.60005
5 Pigment cells ENSDARG00000006008 (dct) marker DOI:10.7554/eLife.60005
5 Pigment cells ENSDARG00000003732 (mitfa) marker DOI:10.7554/eLife.60005
6 Neuron ENSDARG00000033655 (stmn1b) marker DOI:10.7554/eLife.60005
6 Neuron ENSDARG00000014420 (elavl3) marker DOI:10.7554/eLife.60005
6 Neuron ENSDARG00000045639 (elavl4) marker DOI:10.7554/eLife.60005
8 Pigment cells ENSDARG00000071475 (aox5) marker DOI:10.7554/eLife.60005
10 Pigment cells ENSDARG00000062688 (gpnmb) marker DOI:10.7554/eLife.60005
11 Glia ENSDARG00000009823 (pou3f1) marker DOI:10.7554/eLife.60005
11 Glia ENSDARG00000103732 (plp1a) marker DOI:10.7554/eLife.60005