Extended Data Fig. 1: Experiment setup and pre-gating strategy for downstream analysis of the CD11b + myeloid compartment in sdLNs and CNS during EAE.

a, Schematic representation of the experimental approach and the EAE time course used for the experiment. C57BL/6 mice were actively immunized with MOG35-55 emulsified in CFA (day 0, s.c.) and pertussis toxin (days 0 and 2) to induce EAE. Cells were isolated from the sdLN and the CNS from EAE mice at the indicated time points from day 0 to day 20 p.i. and flow cytometry analysis was carried out, n = 2 day 0 and n = 5 day 2⁻20. b, Gating strategy for myeloid cells in sdLN and CNS of MOG35-55 immunized mice before dimensionality reduction and clustering. c, Representative flow cytometry plots showing the strategy to gate on Ly6Chi monocytes, moDCs and moMACs in sdLN and in the CNS at different stages of EAE development. d, Representative contour plots showing NOS2, pro-IL⁻1β and Arginase-1 producing CD11b + and CD88 + cells in the CNS. e, Frequencies of pro-IL-1β, Arginase-1 and NOS2 among Ly6Chi monocytes, moMACs and moDCs in the CNS across the indicated time points (n = 2 for day 0 and n = 5 day 2 to 20 p.i.). f, Continuous time course of relative frequencies of pro-IL-1β + , Arginase-1+ and NOS2 + cells among CD11b + cells from sdLN and CNS, the mean value (centerline) ± s.d. (colored area) (n = 2, day 0 and n = 5, day 2-20 p.i.).