Multiparameter Flow Cytometric Analysis

Cells were stained using a live-dead dye (Supplementary Tables 4 and 5) following the instructions of the manufacturer. Unspecific Fc receptor binding in all single-cell suspensions was blocked by using anti-mouse CD16/CD32 antibody (clone 93, Biolegend, San Diego, CA, USA). Cells were stained for the markers of interest using fluorochrome-conjugated antibodies (Supplementary Tables 4 and 5). All antibodies were diluted from stock concentration according to the ratios reported in Supplementary Tables 4 and 5. For staining of FoxP3, the FOXP3 Fix/Perm Buffer Set (BioLegend) was used following the instructions of the manufacturer. For intracellular cytokine staining, the eBioscience™ Invitrogen™ Intracellular Fixation & Permeabilization Buffer Set (Thermo Fisher Scientific, Waltham, MA, USA) was used following the instructions of the manufacturer. Samples were run on FACSCanto II, LSR Fortessa (BD BioSciences, San Jose, CA, USA) (data was collected using BD FACSDiva 8.0.2) or CytoFLEX LX (Beckman Coulter, Brea, CA, USA) (data was collected using CytExpert 2.4); alternatively, the cells were sorted directly into RLT lysis buffer (Qiagen) using FACS AriaIII (BD BioSciences). Data were analyzed using FlowJo version 10.5.3 (FlowJo LLC, Ashland, OR, USA) or Cytosplore version 2.2.1^{56 (link),57 (link)}. Gating strategies used in this paper can be found in Supplementary Figs. 12 and  13.