Human blood samples were obtained either from Research Blood Components (MA, USA) for technical validation experiments or from collections at the Brigham and Women’s Hospital (MA USA) (table S1). Research on the samples was approved by Institutional Review Boards at the Broad Institute of Massachusets Institute of Technology (MIT) and Harvard (MA, USA) and Brigham and Women’s Hospital (MA, USA). Blood samples from patients with SLE and healthy control donors were drawn with EDTA Vacutainer tubes (BD Biosciences) and processed within 3 hours of collection.

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