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. 2020 Apr 14;9:e53085. doi: 10.7554/eLife.53085

Figure 3. Developmental landscape of tracheal epithelial cells.

(A) ​Horizontal bar graphs showing the cellular composition of mouse tracheal epithelial cells from different developmental and neonatal time points. (B) Violin plots showing the expression of Trp63, Spdef, Creb3l1, and Foxj1 in epithelial cells at different developmental time points. Gene expression has been normalized and log-transformed. (C) scGPS showing cell-cycle gene expression in epithelial cells at different time points. scGPS (single-cell Geneset Percentile Score) is an expression enrichment analysis that utilizes sets of genes underlying certain biological and pathological processes to infer functional profiles for each cell. The cell cycle gene list can be found in Figure 3—source data 1. (D) Heat maps showing transcriptional profiles of tracheal basal, ciliated, and secretory cells across different developmental time points, with age compositions of corresponding cell states showed in horizontal bar plots. Gene expression has been normalized, log-transformed, and z-score transformed. Cell clusters are not predefined by developmental time-points. (E) Pathways enriched in immature and mature secretory cells revealed by gene ontology analysis. Selected top terms for biological process are shown. (F) Pathways enriched in immature and mature ciliated cells revealed by gene ontology analysis. Selected top terms for biological process are shown.

Figure 3—source data 1. Gene Lists for scGPS analysis for cell cycle scoring.

Figure 3.

Figure 3—figure supplement 1. ​ Conserved precursor states of ciliated cells.

Figure 3—figure supplement 1.

(A) Expression of ​Foxn4,​ ​Shisa8​, ​Mcidas,​ and​ Foxj1 ​in early E16 and late E16 tracheal cells detected by RNA FISH. Nuclei are stained by DAPI (white). Scale bar indicates 20 μm. (B) Quantification of ​Shisa8​+ ​/​Foxj1+ ​cells and ​Mcidas+/Foxj1+ ​cells in early (8am dissection) and late (10pm dissection) E16 trachea in the wild-type. Three littermates for each stage were included in analysis. P-value (unpaired t-test) are indicated. Error bars represent S.D. n = 3 for each genotype. (C) A heat map showing state-specific marker genes of ciliated cells at human fetal stage 21–23 GW. Gene expression has been normalized, log-transformed, and z-score transformed. (D) RNA FISH validation of ​FOXN4​ expression, co-localized with a subset of FOXJ1+ ​ cells, in human fetal trachea at 15 GW. Scale bars indicate 20 μ​m.