Fig. 2: scRNA-Seq trajectory recapitulates the airway proximal-distal pattering. | Nature Communications

Fig. 2: scRNA-Seq trajectory recapitulates the airway proximal-distal pattering.

From: FGFR signaling establishes spatial gradients of secretory cell identities along the airway proximal-distal axis

Fig. 2: scRNA-Seq trajectory recapitulates the airway proximal-distal pattering.

A Diffusion-map of secretory cell clusters. Colors and numbers as in Fig. 1C. Line: estimated pseudotime-trajectory by Slingshot. (B) Heatmap of the 1563 differentially expressed genes (FDR < 0.001 and meanLogFC > 1) along pseudotime, based on tradeSeq. AssociationTest of TradeSeq was used for unadjusted p-value calculation, and FDR was estimated with Benjamini & Hochberg correction. The dendrogram of hierarchical clustering (left) indicates 10 stable gene-modules. Bootstrapping values: module-1: 0.65, module-2: 0.62, module-3: 0.61, module-4: 0.74, module-5: 0.68, module-6: 0.75, module-7: 0.8, module-8: 0.7, module-9: 0.64, module-10: 0.9. Color intensity: scaled expression. Dark red: high, Gray: low. C Heatmap of the aggregated expression scores of the genes in the indicated biological processes (Supplementary Data 3). The number after “m” indicates the module containing the genes in (B). Cells were ordered according to pseudotime (Fig. 2A). Red: high, blue: low. D Heatmap of the top-5 genes (according to “waldStat” score in AssociationTest of TradeSeq) of the indicated biological processes in (C). Cells were ordered according to pseudotime. Color: scaled expression (red: high, blue: low). E Heatmap of the selected S1 (cluster-5) and S2 (cluster-1) markers in scRNA-Seq dataset, ordered along pseudotime. Expression levels: log2(normalized UMI-counts+1) (library size was normalized to 10.000). F Left panel: (left) Representative adult mouse lung section stained with DAPI (gray) showing examples of imaged areas along the PD-axis. (Right-up) Cartoon of airway domain classification approach. (Right-bottom) Synopsis of analyzed cell-ROIs from three animals, for the indicated domains (n = 3). Right panel: Heatmap of 3096 analyzed airway secretory cell-ROIs, showing the log2(SCRINSHOT dots +1) signal for the selected markers. Cell-ROI ordering is based on hierarchical clustering. Annotation bars show the (i) airway domains of the cell-ROIs, (ii) the analyzed mouse, and (iii) the indicated cluster. Cluster-A: P-domain cells 38.61 ± 6.89%, I1-domain cells 21.61 ± 2.46%. Cluster-B: I2-domain cells 37.79 ± 7.54%. Cluster-C: I3-domain cells 52.08 ± 6.57%, D-domain cells 69.49 ± 2.20%. Source data are provided as a Source Data file.

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