SCITO-seq: single-cell combinatorial indexed cytometry sequencing

• Published in: Nature methods Vol. 18; no. 8; pp. 903 - 911
• Main Authors: Hwang, Byungjin, Lee, David S., Tamaki, Whitney, Sun, Yang, Ogorodnikov, Anton, Hartoularos, George C., Winters, Aidan, Yeung, Bertrand Z., Nazor, Kristopher L., Song, Yun S., Chow, Eric D., Spitzer, Matthew H., Ye, Chun Jimmie
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.08.2021; Nature Publishing Group
• Subjects: 631/61; 631/61/514/2008; Antibodies; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Case-Control Studies; Cell surface; Cellular proteins; Combinatorial analysis; Cytometry; Deoxyribonucleic acid; DNA; DNA barcoding; DNA sequencing; Droplets; Flow Cytometry - methods; Gene expression; Gene Expression Profiling; High-Throughput Nucleotide Sequencing - methods; Humans; Identification and classification; Life Sciences; Methods; Microfluidics; Microfluidics - methods; Oligonucleotides; Protein composition; Protein research; Proteins; Proteomics; Sequence Analysis, RNA - methods; Single-Cell Analysis - methods; Single-cell protein; Splints; Transcriptome; Transcriptomes; Workflow; United States
• ISSN: 1548-7091; 1548-7105; 1548-7105
• DOI: 10.1038/s41592-021-01222-3

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 protein abundances from thousands of cells simultaneously. As compared to flow and mass cytometry, the high per cell cost of current dsc-seq-based workflows precludes their use in clinical applications and large-scale pooled screens. Here, we introduce SCITO-seq, a workflow that uses splint oligonucleotides (oligos) to enable combinatorially indexed dsc-seq of DNA-barcoded antibodies from over 10 5 cells per reaction using commercial microfluidics. By encoding sample barcodes into splint oligos, we demonstrate that multiplexed SCITO-seq produces reproducible estimates of cellular composition and surface protein expression comparable to those from mass cytometry. We further demonstrate two modified splint oligo designs that extend SCITO-seq to achieve compatibility with commercial DNA-barcoded antibodies and simultaneous expression profiling of the transcriptome and surface proteins from the same cell. These results demonstrate SCITO-seq as a flexible and ultra-high-throughput platform for sequencing-based single-cell protein and multimodal profiling. Single-cell combinatorial indexed cytometry sequencing (SCITO-seq) combines split-pool indexing and droplet-based single-cell sequencing for single-cell protein profiling.