Fig. 2

AECs, but not SECs, express high levels of canonical niche factors. a Representative FACS plot of AECs and SECs from Nestin-GFP mice. SECs, Nestin-GFP^bright AECs and Nestin-GFP^dim AECs were sorted for RNA sequencing. b Principal component analysis of gene expression, showing that Nestin-GFP^bright AECs and Nestin-GFP^dim AECs cluster together, while SECs occupy a space different from AECs. c Hierarchical clustering of significantly differentially expressed genes. The values shown are z-scores. d Heatmap of the genes specific in AECs. Groups are indicated by the colour of the bar on top of the graph as used in panels (a), (b), and (c). The values are log10 transformed-RPKM. e qPCR was performed on sorted AECs and SECs to quantify mRNA levels of Bmx. n = 7 for AECs and SECs. f qPCR was performed on sorted AECs and SECs to quantify mRNA levels of Efnb2. n = 7 for AECs and SECs. g Heatmap of genes specific in SECs. Groups are indicated by the colour of the bar on top of the graph as used in panel c. The values are log10 transformed-RPKM. h Heatmap of niche genes. Different groups are indicated by the colour of the bar on top of the graph as used in panels (a), (b), and (c). The values are log10 transformed-RPKM. i qPCR was performed on sorted AECs and SECs to quantify mRNA levels of Scf. n = 11 for AECs and SECs. j qPCR was performed on sorted AECs and SECs to quantify mRNA levels of Cxcl12. n = 12 for AECs and SECs. k Representative FACS plot of Scf-GFP reporter activity in AECs and SECs. l Representative FACS plot of Cxcl12-GFP reporter activity in AECs and SECs. e, f, i, j Data are represented as mean ± SEM. Data were analysed with two-tailed t-test. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001