Decoding Expression Dynamics of Protein and Transcriptome at the Single Cell Level through Multi-Omics Sequencing in Paired Picoliter Chambers

Simultaneous analysis of mRNAs and proteins at the single-cell level provides information about the dynamics and correlations of gene and protein expressions in individual cells, enabling comprehensive study of cellular heterogeneity and expression patterns. Here, we present a platform for high-throughput cellular indexing of mRNAs and proteins, named multi-Paired-seq, with high cell utilization, accurate molecular measurement and low cost. Based on hydrodynamic differential flow resistance, multi-Paired-seq largely improves cell utilization (>95%). Combined with pump/valve structure, cell-free antibodies and mRNAs can be removed completely for highly accurate detection. The picoliter reaction chambers allow higher detection sensitivity and lower sequencing cost. By using multi-Paired-seq, more elaborate classifications of breast cancers are identified according to multimodal measurements, and the expression correlations between mRNAs and proteins under altered conditions are quantified. Multi-Paired-seq provides multi-modal measurements at the single cell level, which offers a new tool for cell biology, developmental biology, drug discovery and precision medicine. mRNA profiles of different cancer cell lines.