Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling

High-throughput multiomic profiling of single cells by sequencing is a powerful technique for investigating the cellular diversity in complex biological systems. Throughput, cost-effectiveness, and experimental simplicity are crucial considerations in advancing single-cell sequencing technologies. We developed "Overloading And unpacKing" (OAK), a method that enables robust multiomic profiling of hundreds of thousands of cells in a cost effective manner with high detection sensitivity and low labor intensity. To demonstrate OAK's versatility, we conducted single-cell RNA sequencing (scRNA-Seq), antibody-mediated sample multiplexing, and joint scRNA-Seq and single-cell Assay for Transposase Accessible Chromatin with sequencing (scATAC-Seq) usingcell lines. We then showcased OAK's performance on more complex samples, including in vitro differentiated bronchial epithelial cells and primary retinal tissues. Finally, we employed OAK to trace lineages for over 408,000 melanoma cells during treatment with a RAF inhibitor, Belvarafenib, uncovering transcriptional programs associated with cancer resistance.