Extended Data Fig. 9: Bulk RNA sequencing of sort-purified FAPα expressing LL and SL cell populations from the inflamed hind limb joints of day 9 STIA mice.

a, Gating strategy for flow cytometry based cell sorting from day 9 STIA digested synovia gated on CD45⁻CD31⁻ live cells. Coloured gates correspond to each sort-purified population and the percentage gated cell population is indicated. b, Principal component analysis reveals that each population clusters according to either a SL phenotype or a LL phenotype. Each dot presents a single biological replicate sample and is coloured according to the gating strategy outlined in a. c, The heat map shows the differential expression of the 50 most-significant genes (by P value) for each population (Benjamini-Hochberg adjusted P < 0.1) and reveals distinct transcriptional profiles between THY1⁺ and THY1^– cell populations. d, Expression of specific genes RNA sequencing in PDPN⁺FAPα⁺THY1⁻ versus PDPN⁺FAPα⁺THY1⁺ sort-purified cells. For each heat map, a column represents a single biological replicate, coloured according to the gating strategy in a. Biological replicates represent cells isolated and purified from the digestion of synovia from the hind limbs of a single mouse (n = 10 THY1⁻FAPα⁺, n = 5 THY1⁻FAPα⁻, n = 6 THY1⁺FAPα⁻ and n = 12 THY1⁺FAPα⁺ samples).