Additional file 2 of circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics

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Additional file 2: Fig. S1: Amplified TCR cDNA library from a CRC sample visualized on TapeStation; TCR short-read sequencing library quality control; comparison of CBC+CDR3 combinations detected by different VDJ sequencing data-processing pipelines; relationship between sequencing depth and detected TCR clones; and frequency of TCRα or TCRβ chains detected in more than one pairing. Fig. S2: Comparison of clonotype recovery and TCR detection across 5’ immune profiling, 3’ gene expression circVDJ-seq, multiome circVDJ-seq, and MAS-ISO-seq datasets from PBMCs, including replicate overlap, TCR UMI counts, clone sizes, and fraction of T cells with assigned clonotypes. Fig. S3: Venn diagrams showing the overlap of detected CDR3 sequences, spatial barcodes, and CDR3-spatial barcode combinations between circVDJ-seq and long-read Spatial VDJ. Fig. S4: Number of spatial barcodes with a detected TCR chain in circVDJ-seq and long-read Spatial VDJ.

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