Fig. 2: scCOLOR-seq identifies transcript isoform diversity and fusion transcripts in cancer cell line models.

a,b, Human HEK293T and mouse 3T3 cells were mixed at a 1:1 ratio and approximately 1,200 cells were taken for encapsulation and cDNA synthesis followed by nanopore sequencing. a, A Barnyard plot showing the expression of mouse and human UMIs before quality filtering using an edit distance of 6. b, A UMAP plot of data after quality filtering showing the clustering of human, mouse or mixed human and mouse cells after barcode correction using an edit distance of 6. Insets: bar plots show the specificity of UMIs aligning to either the human or mouse UMAP cluster. c–h, NCI-H929, DF15 and JJN3 myeloma cell lines were mixed at a 1:1:1 ratio and approximately 1,200 cells were taken for cDNA synthesis and sequenced using a PromethION flow cell. c,d, UMAP plot of gene expression (c) and transcript isoform expression (d). e, Principal CD74 (also known as HLA-DR) splice variants showing all protein-coding transcripts. f–h, UMAP plot showing the isoform expression of detected CD74 transcripts ENST00000377775.7 (f), ENST00000353334.10 (g) and ENST00000009530.12 (h). i, A UMAP plot of total fusion transcripts in Ewing’s cells mapped as a parentage of the total RNA of the cell. j, A UMAP plot showing the expression of the EWS-FLI fusion transcript. k, A schematic showing the structure of the EWSR1 and FLI1 genes. The EWS-FLI fusion transcript consists of the 5′ end of the EWSR1 gene and the 3′ end of the FLI1 gene. Arrowheads denote known fusion events and the most common type-1 fusion transcript is shown. l, A circular representation of the fusion transcripts identified between FLI1 and EWSR1.