Table 3 Additional marker genes used for cluster annotation.

CD4 + Naive T

CD3D, CD4, CCR7, LEF1, IL6ST, TCF7, TRABD2A, LRRN3

CD4 + Activated T

CD3D, CD4, USP10, IL1B, IL7R, RCAN3, AQP3, TRAC, CAMK4, TCF7

CD4 + Low quality T

CD3D^low, CD4^low, CD3E, RORA, IL2RG, LRP1B, COMMD1, high Percent_mt

CD4 + Memory T

CD3D, CD4, CD40LG, LTB, GATA3, IL7R, CD69, CD28, KLRB1, FAS

CD8 + Naive T

CD3D, CD8A, CD8B, CCR7, LEF1, TRABD2A, TCF7, NELL2, LRRN3

CD8 + Memory T

CD3D, CD8A, CD8B, GZMK, GZMA, CCL5, EOMES, KLRB1, CD69

CD8 + Teff

CD3D, CD8A, CD8B, GZMA, GZMH, CCL5, CST7, GNLY, ZNF683, TBX21

Exhausted T

CD3D^low, TOX, RORA, STAT4, NFAT5, NFATC3, ZAP70, high Percent_mt

NKT

CD3D, CD8A, CD8B, NCAM1, NCR1, TRBC1, GNLY, TRDC

NK

KLRF1, NCAM1, NCR1, NCR3, GNLY, PRF1, KLRD1, CX3CR1, NKG7

Proliferating T/NK

CD3D, CD3G, KLRD1, MKI67, TOP2A, CENPF, CENPE, STMN1

Autophagic cells

ATG7, SLC8A1, FOXO1, DPYD, LRMDA, AOH, SIK3, MYO1F, NOTCH2

Plasma

IGKC, JCHAIN, IGHA1, IGHG1, IGHG3, CD38, MKI67, TNFRSF17

Immature B

CD79A, CD79B, MS4A1, IL7R, BANK1, FAM129C, TNFRSF13C, CCL4

Mature Naive B

CD79A, MS4A1, IGHD, FCER2, BTLA, PAX5, FCRL1, AFF3

Memory B

CD79A, MS4A1, IGHM, IGKC, SWAP70, TFRC, TNFRSF13B/C, AIM2, JCHAIN

Mixed B/Myeloid

IGHM, MS4A1, CD79A, CD14, FCN1, S100A8, S100A9, LYZ

CD14 + TPPP3 + Mono

CD163, CD300E, LYZ, FCN1, CD14, TPPP3, LGALS3, HLA-DRA, HLA-DRB1

CD14 + CYP1B1 + Mono

CD163, CD300E, LYZ, FCN1, CD14, CYP1B1, KLF4, S100A8, S100A9, VCAN

CD14 + IFI + Mono

CD163, CD300E, LYZ, FCN1, CD14, IFI6, IFITM3, IFIT2, IFI44L, OAS2

CD14 + Early Mono

CD163^low, CD300E^low, LYZ, FCN1, CD14, RPL3, RPS27

CD16 + Mono

CD300E, FCN1, FCGR3A, MS4A7, FCER1G, CDKN1C, TCFL2, CD86

moDC

FCER1A, CD1C, HLA-DRA, HLA-DRB1, ITGAX, CLEC10A

pDC

CLEC4C, LILRA4, LILRB4, NRP1, IRF4, IRF7, IRF8

Neutrophils

G0S2, CXCL8, AQP9, ICAM1, CD55, RETN, IL1B^high

Platelets

PF4, TUBB1, PPBP, CAVIN2, SPARC, NRGN, MPIG6B

HSPC

SOX4, CD34, SPINK2, MYB, GATA2, SMIM24