Tapestri Single Cell DNA Sequencing

Cell lines were trypsinized for 2–3 minutes, washed in room temperature Mg²⁺/Ca²⁺-free DPBS, centrifuged at 300g for 5 minutes, and resuspended in DPBS at a concentration of 3K cells/uL. For the experiment using the RPE1, SW48, LS513, LoVo, and CL11 cell lines, 600K cells from each cell line were combined, centrifuged at 300g for 5 minutes, and resuspended in Tapestri Cell Buffer at a concentration of 3.5K cells/uL. For the experiment using the RPE1, hPNE, and hCEC cell lines, 45K cells from each cell line were combined, centrifuged at 300 × g for 5 minutes, and resuspended in Tapestri Cell Buffer at a concentration of 4K cells/uL. For the KaryoCreate experiment, ~100K cells from each condition were combined, centrifuged at 300 × g for 5 minutes, and resuspended in Tapestri Cell Buffer at a concentration of 3.4K cells/uL. Cell droplet encapsulation, barcoding, and sequencing library preparation were performed using the Tapestri instrument according to the manufacturer’s instructions (Mission Bio, San Francisco, CA, USA). Sequencing was performed using an Illumina NovaSeq 6000 or NextSeq 500 in 2×150bp paired-end format. After sequencing, deconvolution of barcodes, read counting, and variant calling were handled by the online Tapestri Pipeline (v2.0.2)(26). The pipeline outputs both read counts per probe for each cell and variant allele frequencies for called variants for each cell.