Figure 3.

RNA sequencing of tracheobronchial basal cells from children and adults

(A) Cluster diagram showing the expression of 32 differentially expressed genes with a false discovery rate (FDR) < 0.01 and a log₂ fold change > 1.2 in three pediatric (months of age/sex; 2.5M, 11M, and 14M) and three adult (years of age/sex; 58F, 61F, and 62F) freshly fluorescence-activated cell-sorted EpCAM⁺/PDPN⁺ basal cell samples. Gene order is based on hierarchical clustering based on the similarity in overall expression patterns. Red represents relative expression higher than the median expression and blue represents lower expression.

(B) Pathway analysis was performed on the three pediatric and three adult freshly fluorescence-activated cell-sorted EpCAM⁺/PDPN⁺ basal cell samples using gene set enrichment analysis (GSEA) to interrogate Hallmark pathways from MSigDB. For pathways with FDR < 0.05, normalized enrichment scores are shown. A negative score (blue) represents upregulation of the pathway in the pediatric samples; a positive score (red) represents upregulation in the adult samples.

(C) Cluster diagram showing the expression of 987 differentially expressed genes with a false discovery rate (FDR) < 0.01 and a log₂ fold change > 1.2 in three pediatric (months of age/sex; 3M, 30M, and 83M) and three adult (years of age/sex; 58F, 60F, and 69M) cultured basal cell samples. Cells were cultured on 3T3-J2 mouse embryonic fibroblast feeder layers for two or three passages in epithelial cell culture medium containing Y-27632. Gene order is based on hierarchical clustering based on the similarity in overall expression patterns. Red represents relative expression higher than the median expression and blue represents lower expression.

(D) Pathway analysis was performed on the three pediatric and three adult cultured basal cell samples using gene set enrichment analysis (GSEA) to interrogate Hallmark pathways from MSigDB. For pathways with FDR < 0.05, normalized enrichment scores are shown. A negative score (blue) represents upregulation of the pathway in the pediatric samples; a positive score (red) represents upregulation in the adult samples.