Supplementary Fig. 2: Surface protein and clonotype detection on PBMCs from a healthy donor and a CTCL patient.

a, Transcriptome-based clustering of PBMCs from healthy donor after removing cell doublets. Projected is the protein signal for 36 out of 49 antibodies used to stain the cells, as well as the 2^nd and 3^rd most abundant CD4⁺ or CD8⁺ TCR α/β or the 3^rd, 4^th, 5^th and 6^th most abundant TCR γ/δ clonotype (red). In total, we detected 1,606 TCR α/β clonotypes from 2,796 barcodes and 183 TCR γ/δ clonotypes from 269 barcodes. The top CD4⁺ TCR α/β clonotype (defined by TRB CDR3 sequence: CASSTLQGKETQYF, shown in Fig. 2a) accounts for ~1% of recovered clonotype-associated barcodes. b, Same analysis as panel a, using data from CTCL patient PBMCs. In total, we detected 1,738 TCR α/β clonotypes from 3,857 barcodes, and 87 TCR γ/δ clonotypes from 243 barcodes. Clonal expansion is readily apparent by the top CD4⁺ TCR α/β clonotype (defined by TRB CDR3 sequence: CSARFLRGGYNEQFF, shown in Fig. 2a) present in 36% of cells for which we recovered clonotype information.