Extended Data Fig. 3: Multiplexed GoT-ChA protocol for simultaneous capture of multiple targeted loci.

a, Sanger sequencing traces showing the expected genotypes of OCI-AML3, CA46, HEL, and SET-2 cell lines for NRAS^Q61, TP53^M133, TP53^R248 and JAK2^V617 utilized in the multiplexed-adapted GoT-ChA cell mixing experiment. Extended Data Fig. 2a has JAK2^V617 sequencing traces for HEL and SET-2 cells. b, Accessibility-based UMAP for original GoT-ChA protocol for CA46 (grey), HEL (gold), OCI-AML3 (violet) and SET-2 (green) cells. c, Accessibility-based UMAP for multiplexing-adapted GoT-ChA protocol (Methods) for cell lines from b. d, Differential gene accessibility markers (FDR < 0.05, Log₂FC > 1.25; Wilcoxon rank sum test followed by Benjamini-Hochberg correction) used for cell line identification. e, UMAP coloured by GoT-ChA JAK2^V617 genotypes of each cell as wild type (WT, blue), mutant (MUT, red), or not assignable (NA, grey) for original GoT-ChA (left) and multiplexed-adapted GoT-ChA (right). f-i, Same as panel e, but for NRAS^Q61, TP53^M133, TP53^R248_1 and TP53^R248_2, respectively. j, Percentage of cells genotyped for targeted loci (JAK^V617, NRAS^Q61, TP53^M133, TP53^R248_1 and TP53^R248_2) for either GoT-ChA original or GoT-ChA adapted protocols (Methods). k, Accuracy for targeted loci and protocols as in j (Methods). l, Distribution of percentage of cells for which a given number of targeted loci were captured, for either the GoT-ChA original or multiplex adapted GoT-ChA protocols (Methods). m, Fraction of cells genotyped according to targeted gene accessibility quantile across targeted loci. Accessibility was assessed as normalized scATAC fragments mapping to the gene body; cells with zero scATAC fragments mapped to the targeted gene were assigned to the first quantile.