FIGURE SUMMARY
Title

Single-cell transcriptome analysis of the zebrafish embryonic trunk

Authors
Metikala, S., Casie Chetty, S., Sumanas, S.
Source
Full text @ PLoS One
Fig 1

Single-cell RNA-seq analysis of trunk region in 30 hpf wild type embryos.

(a) A diagram showing trunk dissection and single cell dissociation followed by single-cell RNA-seq analysis. (b) UMAP plot of 20,279 cells identified a total of 22 different cell clusters.
Fig 2

(a) A heatmap showing expression of marker genes expression in different clusters. (b) A dot plot showing the expression of selected genes in different clusters.

Fig 3

UMAP and violin plots showing the expression of (a) cldni and krt4, top markers for epidermis (cell cluster #1); (b) anxa1c and krt5, top markers for periderm (cluster #14).
Fig 5

UMAP and violin plots showing the expression of selected marker genes for melanocytes (cluster #9, a), ionocytes (cluster #7, b), mucus secreting cells (cluster #18, c), floor plate (cluster #12, d) and xanthophores (cluster #11, e).

Fig 6

Analysis of the endodermal and pronephros cluster #17.

(a) UMAP and violin plots showing the expression of top marker genes, cldnc and aldob. (b) UMAP plot showing further subclustering of this group that resulted in 4 cell subclusters. (c) A heatmap showing expression of marker genes in the subclusters. Note that muscle subclusters #1 and 3 are also positive for endodermal/pronephros marker expression.
Fig 7

Analysis of the vascular endothelium cluster #10.

(a) UMAP and violin plots showing the expression of top marker genes, aqp1a.1 and cldn5b. (b) UMAP plot showing further subclustering of this group. 3 subclusters which show transcriptional signature of arterial, venous and EC—muscle were identified. (c,d) UMAP plot showing the expression of selected arterial and venous specific markers within the vascular endothelial cluster. (e) A heatmap showing expression of marker genes in the subclusters.
Fig 8

UMAP and violin plots showing the expression of selected marker genes for red blood cells, (cluster #13, a), macrophages (cluster #16, b), blood cells of unknown identity (cluster #21, c) and lateral plate mesoderm (cluster #6, d).
Fig 9

UMAP and violin plots showing the expression of selected marker genes for two skeletal muscle groups (clusters #4 and #0, a,b), slow muscle (cluster #5, c) and somites (cluster #19, d).
Fig 10

UMAP and violin plots showing the expression of selected marker genes for fibroblast like (cluster #3, a) and notochordal cells (cluster #15, b).
Fig. 4

UMAP and violin plots showing the expression of selected marker genes for spinal cord (cluster #2, a), neurons-1 (cluster #8, b) and neurons-2 (cluster #20, c).

Acknowledgments
This image is the copyrighted work of the attributed author or publisher, and ZFIN has permission only to display this image to its users. Additional permissions should be obtained from the applicable author or publisher of the image. Full text @ PLoS One
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