Highly parallel and efficient single cell mRNA sequencing with paired picoliter chambers

Mingxia Zhang,Mingxuan Gao,Zhi Zhu,Wei Lin,Yuan Zou,Chaoyong Yang,Jia Song,Richard N Zare,Xing Xu,Xuebing Zhang,Peifeng Huang,Qin Chen

doi:10.1038/s41467-020-15765-0

Abstract

ScRNA-seq has the ability to reveal accurate and precise cell types and states. Existing scRNA-seq platforms utilize bead-based technologies uniquely barcoding individual cells, facing practical challenges for precious samples with limited cell number. Here, we present a scRNA-seq platform, named Paired-seq, with high cells/beads utilization efficiency, cell-free RNAs removal capability, high gene detection ability and low cost. We utilize the differential flow resistance principle to achieve single cell/barcoded bead pairing with high cell utilization efficiency (95%). The integration of valves and pumps enables the complete removal of cell-free RNAs, efficient cell lysis and mRNA capture, achieving highest mRNA detection accuracy (R = 0.955) and comparable sensitivity. Lower reaction volume and higher mRNA capture and barcoding efficiency significantly reduce the cost of reagents and sequencing. The single-cell expression profile of mES and drug treated cells reveal cell heterogeneity, demonstrating the enormous potential of Paired-seq for cell biology, developmental biology and precision medicine.

Highlights

ScRNA-seq has the ability to reveal accurate and precise cell types and states
Analysis results of sequencing data for External RNA Controls Consortium (ERCC) suggests that our method offers high accuracy (R = 0.955) and comparable sensitivity compared to other current scRNA-seq platforms
Each reaction unit is designed based on the hydrodynamic differential flow resistance principle to allow no more than one bead and cell to be captured in each bead capture chamber and cell capture chamber, respectively (Fig. 1d, a)

Summary

Introduction

ScRNA-seq has the ability to reveal accurate and precise cell types and states. Existing scRNA-seq platforms utilize bead-based technologies uniquely barcoding individual cells, facing practical challenges for precious samples with limited cell number. We present a scRNA-seq platform, named Paired-seq, with high cells/beads utilization efficiency, cell-free RNAs removal capability, high gene detection ability and low cost. After single-cell isolation, each cell must be processed and sequenced individually to obtain transcriptome information, which is labor intensive and cost prohibitive, especially when a large population of cells is needed to be processed To address this problem, several novel highthroughput platforms have been reported, including Drop-seq[13], inDrop[12], Seq-well[15], and Microwell-seq[14], etc., which used barcoded beads to label individual cells during reverse transcription so that cDNAs from all the cells could be simultaneously pooled for amplification and sequencing[29]. By identifying the cell barcode and molecular index, the cell origin of cDNA could be inferred and the amplification bias could be corrected

Methods

Results

Conclusion