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Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis.

Communications biology (2020-05-10)
Maeve O'Huallachain, Felice-Alessio Bava, Mary Shen, Carolina Dallett, Sri Paladugu, Nikolay Samusik, Simon Yu, Razika Hussein, Grantland R Hillman, Samuel Higgins, Melanie Lou, Angelica Trejo, Laura Qin, Yu Chuan Tai, Shigemi M Kinoshita, Astraea Jager, Deval Lashkari, Yury Goltsev, Sedide Ozturk, Garry P Nolan
ABSTRACT

Single-cell omics provide insight into cellular heterogeneity and function. Recent technological advances have accelerated single-cell analyses, but workflows remain expensive and complex. We present a method enabling simultaneous, ultra-high throughput single-cell barcoding of millions of cells for targeted analysis of proteins and RNAs. Quantum barcoding (QBC) avoids isolation of single cells by building cell-specific oligo barcodes dynamically within each cell. With minimal instrumentation (four 96-well plates and a multichannel pipette), cell-specific codes are added to each tagged molecule within cells through sequential rounds of classical split-pool synthesis. Here we show the utility of this technology in mouse and human model systems for as many as 50 antibodies to targeted proteins and, separately, >70 targeted RNA regions. We demonstrate that this method can be applied to multi-modal protein and RNA analyses. It can be scaled by expansion of the split-pool process and effectively renders sequencing instruments as versatile multi-parameter flow cytometers.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Deoxynucleotide Mix, 10 mM, Molecular Biology Reagent
Sigma-Aldrich
Deoxyribonucleic acid, single stranded from salmon testes, For hybridization