library_construction_protocol: PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample.  Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262).