Table 4.

Additional marker genes used for cell type classification of clusters (level 2).

Level2 annotation – additional markers
Proliferating T/NK	TOP2A, MKI67, NUSAP1
NK	KLRF1, KLRD1, KLRB1, GNLY, NKG7
Naïve T	PTPRC
CD8+ Tem	GZMA, GZMM, CD8
CD4+ Treg	CTLA4, CD4
Mature naïve B	CD22, CD53, CD79A
Plasma	IGHA2, IGHM, TNFRSF17
pDCs	IRF7, IRF8
cDC2/moDCs	CLEC10A
Mast	KIT, CPA3, CD63
Monocytes	CD14, CSF3R
Low quality Mφ	LYZ, FTL, high number of MT- and RPL/S genes
Lipid-associated Mφ	MS4A7, IL1B, IL4I1, FOLR2, APOE, C1QA/B/C, CTSB/D
Alveolar Mφ	MCEMP1, PPARG, MRC1
Proliferating Mφ	CDCA8, MKI67, CENPF, CD14, TOP2A
Neutrophils	FCGR3B, CSF3R, S100A12, S100A8
CDKN2A Cancer	CDK4, PUM3, NTS, EPCAM
SOX2 Cancer	KRT17, S100A2, SFN, PTHLH, PERP
CXCL1 Cancer	SPRR3, AGR2, CEACAM6
LAMC2 Cancer	FGB, FGA, FGG, PAEP, TESC
Proliferating Cancer	MKI67, TOP2A, CENPF, CDC20
Pathological Alveolar	SFTPB, WFDC2, AGR2, AGR3, MUC1
Alveolar	SFTPC, AQP4, SCGB3A1
Ciliated	FOXJ1, CDHR3
CAF	SPARC, FAP, PDGFRB
SMC	ACTA2, CALD1, TAGLN
Endothelial	FLT1, PECAM1