μCB-seq: microfluidic cell barcoding and sequencing for high-resolution imaging and sequencing of single cells

• Published in: Lab on a chip 2020-11, Vol.2 (21), p.3899-3913
• Main Authors: Chen, Tyler N, Gupta, Anushka, Zalavadia, Mansi D, Streets, Aaron
• Format: Article
• Language: English
• Subjects: Biological activity; Chemical composition; Functional integration; Gene expression; Gene Expression Profiling; Gene sequencing; High resolution; Image resolution; Microfluidic devices; Microfluidics; Morphology; Optical measurement; Optical microscopy; Sequence Analysis, RNA; Single-Cell Analysis; Software
• ISSN: 1473-0197; 1473-0189; 1473-0189
• DOI: 10.1039/d0lc00169d

Single-cell RNA sequencing (scRNA-seq) enables the investigation of complex biological processes in multicellular organisms with high resolution. However, many phenotypic features that are critical to understanding the functional role of cells in a heterogeneous tissue or organ are not directly encoded in the genome and therefore cannot be profiled with scRNA-seq. Quantitative optical microscopy has long been a powerful approach for characterizing diverse cellular phenotypes including cell morphology, protein localization, and chemical composition. Combining scRNA-seq with optical imaging has the potential to provide comprehensive single-cell analysis, allowing for functional integration of gene expression profiling and cell-state characterization. However, it is difficult to track single cells through both measurements; therefore, coupling current scRNA-seq protocols with optical measurements remains a challenge. Here, we report microfluidic cell barcoding and sequencing (μCB-seq), a microfluidic platform that combines high-resolution imaging and sequencing of single cells. μCB-seq is enabled by a novel fabrication method that preloads primers with known barcode sequences inside addressable reaction chambers of a microfluidic device. In addition to enabling multi-modal single-cell analysis, μCB-seq improves gene detection sensitivity, providing a scalable and accurate method for information-rich characterization of single cells. We present a platform for on-chip molecular barcoding that combines high-resolution imaging with genomic analysis, enabling multi-modal phenotypic measurements in single cells.