Mass cytometry processing and quality control
CyTOF data were acquired with a CyTOF2 system using a SuperSampler fluidics system (Victorian Airships) at an event rate of < 400 events per second and normalized with Helios normalizer software (Fluidigm version 6.7.1016). Acquisitions from different days (three independent acquisitions were performed) were normalized using five-element beads (Fluidigm). Barcoded samples were deconvoluted and cross-sample doublets were filtered using cytobank application. CyTOF data was pre-processed with Cytobank (https://mtsinai.cytobank.org; Cytobank, 7.0) to sequentially remove calibration beads, dead cells, debris and barcodes for CD45+ PBMCs based on event length, DNA (191Ir and 193Ir) and live cell (195Pt) channels and then export the FCS files. We analyzed 200,000 PBMCs in cohort-1 and 160,000 PBMC in cohort-2, with an average of 20,000 cells per sample.