ECCITE-seq captures transcriptional, surface protein and clonotypic information from multiplexed healthy and CTCL tissues as well as malignant heterogeneity in disease. (A) Representative t-SNE plots of single cells from PBMCs and skin dissociated tissue of a CTCL patient (SS1) clustered and visualized by GEX and ADT expression using WNN analysis and colored by cluster (left) or tissue of origin (right). (B) Dot plot showing the percentage of populations making up the skin and blood of a healthy control (HC1), 5 CTCL patients (SS1-MF stage IV1), and blood from 2 CTCL patients (SS6 and SS7). Apoptotic keratinocytes from skin tissue were filtered out. (C) Representative t-SNE plot depicting transcriptional heterogeneity within the malignant T cells from matched blood and skin defined by their common expanded clonotype in a CTCL patient. (D) Bar plots showing the subclonal composition based on transcriptional differences in malignant T cells from 7 CTCL patients (5 of whom have matched blood and skin). APK, apoptotic keratinocytes; BC, B cells; BCM, memory B cells; DC, dendritic cells; FB, fibroblasts; gdT, γ/δ T cells; KRT, keratinocytes; M, malignant T cells; MO, monocytes/macrophages; NK, natural killer cells; pDC, plasmacytoid dendritic cells; T4M, memory CD4+ T cells; T4N, naïve CD4+ T cells; T8E, effector CD8+ T cells; T8M, memory CD8+ T cells; T8N, naïve CD8+ T cells; UNC, unclassified.