PROJECT ID: GSE152982

Data source GEO: GSE152982
Description Here we performed single-cell RNAseq analysis of whole wildtype zebrafish trunks at 30hpf using 10x Genomics' Chromium platform. 22 distinct cell populations were identified, spanning all three embryonic germ layers.
Key word expression; gene
Publication Metikala S, Casie Chetty S, Sumanas S. Single-cell transcriptome analysis of the zebrafish embryonic trunk. PLoS One 2021;16(7):e0254024. PMID: 34234366
Abstract During embryonic development, cells differentiate into a variety of distinct cell types and subtypes with diverse transcriptional profiles. To date, transcriptomic signatures of different cell lineages that arise during development have been only partially characterized. Here we used single-cell RNA-seq to perform transcriptomic analysis of over 20,000 cells disaggregated from the trunk region of zebrafish embryos at the 30 hpf stage. Transcriptional signatures of 27 different cell types and subtypes were identified and annotated during this analysis. This dataset will be a useful resource for many researchers in the fields of developmental and cellular biology and facilitate the understanding of molecular mechanisms that regulate cell lineage choices during development.


Dataset Information

Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. GSE152982 (wild type) Danio rerio trunk baseline 1.25dpf, untreatment GEO: GSM4631066

Clustering Result

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Skeletal muscle cells ENSDARG00000002768 (pvalb2) marker DOI:10.1371/journal.pone.0254024
1 Skeletal muscle cells ENSDARG00000017441 (mylz3) marker DOI:10.1371/journal.pone.0254024
1 Skeletal muscle cells ENSDARG00000014196 (myl1) marker DOI:10.1371/journal.pone.0254024
1 Skeletal muscle cells ENSDARG00000041065 (hspb1) marker DOI:10.1371/journal.pone.0254024
2 Spinal cord ENSDARG00000053569 (sox3) marker DOI:10.1371/journal.pone.0254024
3 Epidermal cells ENSDARG00000054616 (cldni) marker DOI:10.1371/journal.pone.0254024
4 Slow muscle ENSDARG00000042245 (myl13) marker DOI:10.1371/journal.pone.0254024
4 Slow muscle ENSDARG00000062592 (myl10) marker DOI:10.1371/journal.pone.0254024
5 Fibroblasts ENSDARG00000012405 (col1a1a) marker DOI:10.1371/journal.pone.0254024
5 Fibroblasts ENSDARG00000071586 (tgfbi) marker DOI:10.1371/journal.pone.0254024
6 Neuron ENSDARG00000033655 (stmn1b) marker DOI:10.1371/journal.pone.0254024
7 Lateral mesoderm ENSDARG00000039579 (cfd) marker DOI:10.1371/journal.pone.0254024
7 Lateral mesoderm ENSDARG00000008305 (hand2) marker DOI:10.1371/journal.pone.0254024
8 Ionocytes ENSDARG00000032849 (ndrg1a) marker DOI:10.1371/journal.pone.0254024
8 Ionocytes ENSDARG00000076833 (atp1b1b) marker DOI:10.1371/journal.pone.0254024
9 Vascular endothelium ENSDARG00000023713 (aqp1a.1) marker DOI:10.1371/journal.pone.0254024
9 Vascular endothelium ENSDARG00000014059 (cldn5b) marker DOI:10.1371/journal.pone.0254024
10 Melanophores ENSDARG00000006008 (dct) marker DOI:10.1371/journal.pone.0254024
10 Melanophores ENSDARG00000091298 (pmela) marker DOI:10.1371/journal.pone.0254024
11 Xanthophores ENSDARG00000058734 (prdx1) marker DOI:10.1371/journal.pone.0254024
12 Red blood cells ENSDARG00000087390 (hbbe1.3) marker DOI:10.1371/journal.pone.0254024
12 Red blood cells ENSDARG00000079305 (hbae3) marker DOI:10.1371/journal.pone.0254024
13 Floor plate -- (ctgfa) marker DOI:10.1371/journal.pone.0254024
13 Floor plate ENSDARG00000040159 (wnt4b) marker DOI:10.1371/journal.pone.0254024
14 Periderm cells ENSDARG00000104359 (anxa1c) marker DOI:10.1371/journal.pone.0254024
15 Notochord ENSDARG00000031483 (col9a1b) marker DOI:10.1371/journal.pone.0254024
16 Mucous secreting cells ENSDARG00000070480 (agr2) marker DOI:10.1371/journal.pone.0254024
16 Mucous secreting cells ENSDARG00000037790 (pvalb8) marker DOI:10.1371/journal.pone.0254024
17 Macrophages ENSDARG00000090783 (mfap4) marker DOI:10.1371/journal.pone.0254024
17 Macrophages ENSDARG00000056874 (lygl1) marker DOI:10.1371/journal.pone.0254024