A pseudobulk differential expression analysis (DEA) between IPF and HC samples identified 1,469 differentially expressed genes (DEGs) (Fig. 1d), including genes associated with fibroblasts, previously reported to be upregulated in IPF (FNDC1, COL10A1 and THY1)23, as well as matrix metalloproteinases24 and genes involved in IPF-associated signaling pathways (SFRP2, WNT10A and TGFBI)25,26 (Supplementary Table 2). Here, SFRP2 is linked to idiopathic pulmonary fibrosis.