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. 2022 Apr 19;322(6):L822–L841. doi: 10.1152/ajplung.00254.2021

Figure 1.

Figure 1.

Differentiation of the lung epithelium in vitro induces differential expression of thousands of genes including 1,621 lncRNAs. A: bulk RNA-Seq experimental design. HBECs from eight donors were cultured in submerged cultures and as ALI cultures before analysis by RNA-Seq. B: unbiased clustering of all samples using principal component analysis (PCA). All genes with <1 TPM value (averaged across all samples) were removed before performing PCA, n = 8 donors. C: volcano plot of expressed genes (TPM ≥ 1) between submerged and ALI cultures, n = 8 donors. Red dots, adjusted P value <10−6 and log2 fold-change >2; blue dots, adjusted P value <10−6 and log2 fold-change <2; black dots, adjusted P value >10−6 and log2 fold-change >2; orange dots, >10−6 and log2 fold-change <2. D: lung epithelial markers, TPM values plotted as heatmap between submerged (SUB) and ALI cultures, n = 8 donors. E: MA plot of protein coding (PC) and long noncoding RNA (lncRNA) expression between submerged and ALI cultures, n = 8. F: density plot depicting expression of PC and lncRNAs. Plotted are log2 TPM values averaged across submerged and ALI cultures from all donors, n = 8 donors. ALI, air-liquid interface; HBECs, human bronchial epithelial cells; PC, protein coding.