Supporting information tables.

Table A in S1 Text. Demographic and clinical characteristics of the four patients analysed. Continuous variables are presented as mean ± SD. Discrete variables are presented as n (%). Table B in S1 Text. Characteristics of the lung specimens and single cell/nucleus suspensions. Table C in S1 Text. Number of cells/nuclei identified at each hierarchical level (level 1–5, 61 cell types defined at the finest level by the HLCA). Thirty-five finest level cell types were recovered with >100 cells (51 finest level cell types with at least one cell identified). Here unclassified refers to cells/nuclei which could not be assigned confidently to the specific annotation level (annotation score < 0.5). Table D in S1 Text. Differentially Expressed Genes (Normal Cell versus Normal Nucleus samples). Table E in S1 Text. Differentially Expressed Genes (Normal Cell versus Tumor Cell samples). Table F in S1 Text. Differentially Expressed Genes (Normal Nucleus versus Tumor Nucleus samples). Table G in S1 Text. Differentially Expressed Genes (Tumor Cell versus Tumor Nucleus samples). Table H in S1 Text. Differentially Expressed Gene Ontology terms (Biological Process). Table I in S1 Text. Benchmarking scRNA-seq and snRNA-seq methods in paired normal-adenocarcinoma lung samples using the 10x Genomics workflows. Table J in S1 Text. 10X Genomics Cell Ranger software—QC metrics. (XLSX)