Open AccessSCITO-seq: single-cell combinatorial indexed cytometry sequencing
Author(s) -
Byung Kook Hwang,
David Lee,
Whitney Tamaki,
Yang Sun,
Anton Ogorodnikov,
George Hartoularos,
Aidan Winters,
Bertrand Z. Yeung,
Kristopher L. Nazor,
Yun S. Song,
Eric D. Chow,
Matthew H. Spitzer,
Chun Jimmie Ye
Publication year - 2021
Publication title -
nature methods
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 19.469
H-Index - 318
eISSN - 1548-7105
pISSN - 1548-7091
DOI - 10.1038/s41592-021-01222-3
Subject(s) - mass cytometry , oligonucleotide , workflow , computational biology , flow cytometry , dna sequencing , biology , dna , cytometry , cell , microfluidics , microbiology and biotechnology , computer science , nanotechnology , gene , genetics , materials science , database , phenotype
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.