Supplementary Figure 5: PIC-seq in the postnatal lung.

a, FACS plot of EPCAM⁺ (CD326) epithelial cells, CD45⁺ immune cells and PIC derived from postnatal murine lung. Results are representative of two independent experiments. b, Gene expression profiles of 1,071 CD45⁺ or EPCAM⁺ single cells from postnatal lungs, grouped into 13 cell types. Top panel indicates UMI count. c, CD45⁺ and EPCAM⁺ cell subset identity of single cells in a. d, Gene expression profiles of 543 PICs, grouped by their contributing CD45⁺ and EPCAM⁺ identities, as determined by PIC-seq algorithm. Top panels as in a. e, CD45⁺ and EPCAM⁺ subset identities of PIC contributing cells in b, as determined using the PIC-seq algorithm. f, Estimation of the relative UMI count from epithelial cells (green), and immune cells (red) contributing to each PIC in b, as inferred using the PIC-seq algorithm (mixing factor). g-h, Differences in metacell composition between PIC contributing epithelial cells (g) and PIC contributing immune cells (h) in postnatal lungs. Each bar represents one metacell, and shows log₂ fold change of its frequency between the PIC and the EPCAM⁺ (g) or CD45⁺ (h) single-cell populations. Bar colors relate to metacell subset identity. i, Distribution of Epcam⁺ and CD45⁺ subsets in non-conjugated populations and in PICs. Two-tailed FDR adjusted Fisher’s exact test; n= 621 Epcam⁺, 441 CD45⁺ single cells, and 543 PICs. j, Mean observed (gray bar) and expected (colored bar) gene expression of Alveolar type 1 (AT1)-C45⁺ PICs grouped by subsets of C45⁺ contributing cells (x-axis). Error bars indicate binomial 95% confidence intervals of the observed values. n=543 PICs.