Fig. 4: Demographic and technical variables driving interindividual variation.

a, Fraction of total inter-sample variance in the HLCA core integrated embedding that correlates with specific covariates. Covariates are split into technical (left) and biological covariates (right). Cell types are ordered by the number of samples in which they were detected. Only cell types present in at least 40 samples are shown. Tissue sampling method represents the way a sample was obtained (for example, surgical resection or nasal brush). Donor status represents the state of the donor at the moment of sample collection (for example, organ donor, diseased alive or healthy alive). The heatmap is masked gray where fewer than 40 samples were annotated for a specific covariate or where only one value was observed for all samples for that cell type. b, Selection of gene sets that are significantly associated with anatomical location CCF score, in different airway epithelial cell types. All gene set names are Gene Ontology biological process (GO: BP) terms. Sets upregulated toward distal lungs are shown in green, whereas sets downregulated are shown in blue. The full name of the term marked by an asterisk is ‘Antigen processing and presentation of exogenous peptide antigen via MHC-I’. c, Cell type proportions per sample, along the proximal-to-distal axis of the respiratory system. The lowest and highest CCF scores shown (0.36 and 0.97) represent the most proximal and most distal sampled parts of the respiratory system, respectively (trachea and parenchyma), excluding the upper airways. The dots are colored by the tissue dissociation protocol and tissue sampling method used for each sample. The boxes show the median and interquartile range of the proportions. Samples with proportions more than 1.5 times the interquartile range away from the high and low quartile are considered outliers. Whiskers extend to the furthest nonoutlier point. n = 23, 19, 9 and 90 for CCF scores 0.36, 0.72, 0.81 and 0.97, respectively. d, Selection of gene sets significantly up- (green) or downregulated (blue) with increasing BMI, in four different cell types. For b and d, P values were calculated using correlation-adjusted mean-rank gene set tests (Methods) and false discovery rate corrected using the Benjamini–Hochberg procedure. IL-1, interleukin-1; MHC-I, major histocompatibility complex class I; TNF, tumor necrosis factor.