RT Journal Article SR Electronic T1 Quantification of proteins, protein complexes and mRNA in single cells by proximity-sequencing JF bioRxiv FD Cold Spring Harbor Laboratory SP 2020.05.15.098780 DO 10.1101/2020.05.15.098780 A1 Luke Vistain A1 Hoang Van Phan A1 Christian Jordi A1 Mengjie Chen A1 Sai T. Reddy A1 Savaş Tay YR 2020 UL http://biorxiv.org/content/early/2020/05/16/2020.05.15.098780.abstract AB Multiplexed analysis of single-cells enables accurate modeling of cellular behaviors, classification of new cell types, and characterization of their functional states. Here we present proximity-sequencing (Prox-seq), a method for simultaneous measurement of an individual cell’s proteins, protein complexes and mRNA. Prox-seq utilizes deep sequencing and barcoded proximity assays to measure proteins and their complexes from all pairwise combinations of targeted proteins, in thousands of single-cells. The number of measured protein complexes scales quadratically with the number of targeted proteins, providing unparalleled multiplexing capacity. We developed a high-throughput experimental and computational pipeline and demonstrated the potential of Prox-Seq for multi-omic analysis with a panel of 13 barcoded proximity probes, enabling the measurement of 91 protein complexes, along with thousands of mRNA molecules in single T-cells and B-cells. Prox-seq provides access to an untapped yet powerful measurement modality for single-cell phenotyping and can discover new protein interactions in signaling and drug studies.Competing Interest StatementThe authors have declared no competing interest.