Mass Cytometry Data Analysis
RESIDUAL
Data were normalized with EQ-normalization passport for each experiment. Subsequently, the data were gated using Flowjo v10.6.1, using channels 89Y_CD45, 193Ir_DNA, Residual, 103Rh_DNA (live/dead) and 140Ce_bead, removing debris, dead cells and doublets. Next, the data were compensated and debarcoded in R v4.1.1 using the CATALYST package and automatic cutoffs. The data were arcsin 5 transformed in Cytosplore. Using the reference sample, the data were corrected for batch effects using R after which the data were downsampled to a maximum of 50.000 cells/sample. For the discovery analysis the FlowSOM package was used [