Science Advances

Supplementary Materials

The PDFset includes:

  • Table S1. Bronchial brushings were procured from six never smokers and six current smokers.
  • Table S2. Bronchial tissue was obtained by lung resection from four never smokers and four current smokers at the UMCG.
  • Table S3. Bronchial tissue was obtained by lung resection from five never smokers and five current smokers at the UCL Hospital.
  • Fig. S1. Single bronchial cells were isolated by FACS.
  • Fig. S2. scRNA-Seq data quality were evaluated for each donor.
  • Fig. S3. Low-quality cells were excluded from downstream analyses.
  • Fig. S4. Bronchial brushings reconstructed in silico from single-cell data resemble data generated from bulk bronchial brushings.
  • Fig. S5. LDA was used to identify Cell-States and Gene-States.
  • Fig. S6. Gene-State and Cell-State model optimization.
  • Fig. S7. LDA was used to identify 13 cell clusters.
  • Fig. S8. LDA was used to identify 19 gene sets.
  • Fig. S9. Gene set expression across cell clusters.
  • Fig. S10. T cell receptor genes were detected in CD45+ cell cluster.
  • Fig. S11. Cluster 13 cells expressed CFTR.
  • Fig. S12. Distributions of cell clusters within each subject.
  • Fig. S13. Smoking-associated differential expression of each gene set was analyzed in published bulk bronchial brushing data.
  • Fig. S14. Nonciliated cell AKR1B10 expression was uncommon.
  • Fig. S15. MN and GCH tissue regions were distributed throughout the bronchial airways of current smokers.
  • Fig. S16. Basal cell numbers were not altered in smokers.
  • Fig. S17. Increased numbers of indeterminate KRT8+ cells were observed in GCH smoker tissue.
  • Fig. S18. PG cells were enriched in regions of GCH within the airways of smokers.
  • Fig. S19. Smoking-induced heterogeneity was observed in the human bronchial epithelium.

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Other Supplementary Material for this manuscript includes the following:

  • Extended table S1 (Microsoft Excel format). Primer sequences for scRNA-Seq.
  • Extended table S2 (Microsoft Excel format). Statistical modeling results, State Specificity, and State Similarity values for all genes.
  • Extended table S3 (Microsoft Excel format). Functional annotation results for each gene set.

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