Extended Data Fig. 5: Flow-cytometric validation of STM clustering categorized by scRNAseq.

a–c, scRNAseq data (a) (patient cohort described in Fig. 2a) and flow cytometry data (b-c) representing 16 independent experiments with synovial tissue samples from 31 RA patients and 10 Healthy showing that mRNA and protein expression of MerTK and FOLR2 coincide, suggesting that FOLR2 can be used as an alternative marker of MerTK^pos STMs. d, Representative gating strategies for TREM2 and LYVE1 positive STMs in conjunction with MerTK expression in health, active RA and RA in disease remission. The TREM2^pos cluster is defined by the positive expression of MerTK and TREM2, and the LYVE1^pos cluster is defined by the positive expression of LYVE1 and MerTK. A proportion of TREM2^pos STMs are also LYVE1^pos. The n numbers per staining and quantitative data are provided in Fig. 2i-k. e-g, scRNAseq data (e) (patient cohort described in Fig. 2a) and representative gating strategy for MerTK^neg STMs (f) showing that most of MerTK^neg STMs are CD48 positive. g, Distribution of CD9 and CLEC10a positive cells within MerTK^negCD48^low/pos STMs in health, active RA and RA in disease remission are shown. The MerTK^negS100A12^pos cluster is defined as CD48^low/posCD9^negCLEC10a^neg; the MerTK^negSPP1^pos cluster is defined as CD48^pos/lowCD9^posCLEC10a^neg, and the MerTK^negCLEC10a^pos cluster is defined as CD48^low/posCD9^posCLEC10a^pos. The n numbers per staining and quantitative data are provided in Fig. 2i-k.