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SCITO-seq: single-cell combinatorial indexed cytometry sequencing

By Byungjin Hwang, David S Lee, Whitney Tamaki, Yang Sun, Anton Ogorodnikov, George Hartoularos, Aidan Winters, Yun S. Song, Eric D. Chow, Matthew H. Spitzer, Chun Jimmie Ye

Posted 30 Mar 2020
bioRxiv DOI: 10.1101/2020.03.27.012633

The development of DNA-barcoded antibodies to tag cell-surface molecules has enabled the use of droplet-based single cell sequencing (dsc-seq) to profile the surface proteomes of cells. Compared to flow and mass cytometry, the major limitation of current dsc-seq-based workflows is the high cost associated with profiling each cell, thus precluding its use in applications where millions of cells are required. Here, we introduce SCITO-seq, a new workflow that combines combinatorial indexing and commercially available dsc-seq to enable cost-effective cell surface proteomic sequencing of greater than 105 cells per microfluidic reaction. We demonstrate SCITO-seq's feasibility and scalability by profiling mixed species cell lines and mixed human T and B lymphocytes. To further demonstrate its applicability, we show comparable cellular composition estimates in peripheral blood mononuclear cells obtained with SCITO-seq and mass cytometry. SCITO-seq can be extended to include simultaneous profiling of additional modalities such as transcripts and accessible chromatin or tracking of experimental perturbations such as genome edits or extracellular stimuli.

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