Cite-seq with TCR: CD4 and CD8 T cells were isolated from kidney, spleen, and renal lymph node of lupus-prone MRL/MpJ-Faslpr/J or MRL/MpJ-Faslpr/J.Nur77-eGFP (sorted on eGFP expression). Single cells were encapsulated in Gel-Beads-in-Emulsion (GEMs) using the 10x Genomics Chromium Controller and Chromium Single Cell 5′ chemistry (5P HT v2 Next-GEM). Multiome: CD44hi T cells were isolated from  kidney, spleen and renal lymph node of lupus-prone MRL/MpJ-Faslpr/J mice. Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10x Genomics Chromium Controller with the Chromium Single Cell Multiome ATAC + Gene Expression kit. Library preparation and sequencing were performed at the Yale Center for Genome Analysis (YCGA). The 10x Single Cell 5' with Feature Barcoding and Immune Receptor Mapping protocols (CG000330 Rev F,  CG000208 Rev G) with TotalSeq™-C cell hashing (HTO) was used to generate 5′ gene expression, TCR V(D)J enrichment , and  HTO (hashtag) libraries. The Single Cell Multiome ATAC + Gene Expression portocol described by 10X Genomics (CG000338 Rev G) was used to generate 3' gene expression library and ATAC libraries.