Mass cytometry

Cryopreserved PBMC from SLE and matched HC were processed and analyzed as previously published⁵⁸. Lists of mass cytometry antibodies are provided in the Supplementary Table ² and were previously described⁵⁸. To avoid batch effect, PBMCs of SLE and matched HC were barcoded, processed, and examined at the same time. Manual gating of FCS files was performed using FlowJo™ Software version 10.7.1 (Becton, Dickinson and Company; 2019⁵⁹) on all cell populations from each samples. High dimensional data analysis was performed by exploiting the following FlowJo™ plugins: DownSample v3.3 and FlowSOM⁶⁰ v2.9. Dimensionality reduction was realized using the Barnes-Hut implementation of t-stochastic neighboring embedding (t-SNE) algorithm on downsampled samples to obtain equal number of cells in SLE patients and HC. This is a common strategy used to analyze high dimensional data in mass cytometry analysis⁶¹. Unsupervised clustering analysis was performed using self-organizing map in combination with consensus clustering (FlowSOM) using 100 clusters.