MICROFLUIDIC CELL BARCODING AND SEQUENCING

MICROFLUIDIC CELL BARCODING AND SEQUENCING

Researchers at UC Berkeley have developed µCB-seq, a microfluidic cell barcoding and sequencing platform for high-resolution imaging and sequencing of single cells.

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 expression and localization, and organelle dynamics.

Stage of Research

The inventors have developed µCB-seq, a microfluidic cell barcoding and sequencing platform that combines optical imaging and scRNA-seq to allow for functional integration of gene expression profiling and cell-state characterization. In CB-seq, a known library of barcoded nucleic acid capture primers is printed into specified microfluidic chambers during fabrication. Therefore, single cell transcriptomes can be deterministically demultiplexed and linked to a chamber’s spatial location on the device, allowing for the combination of high-resolution imaging and sequencing data from the same cell.

Applications

• Multiplexed acquisition of both imaging-based and genomic readouts from single cells by associating known barcodes with single cells in a deterministic fashion

Advantages

• µCB-seq platform combines the flexibility of valve-based microfluidics with the efficiency of multiplexed RNA-seq protocols
• Compatible with high-resolution or time-resolved imaging, enabling characterization of dynamic phenotypic information
• Device is modular and scalable, and is compatible with other non-invasive or non-perturbative single cell measurements

Stage of Development

Research – in vitro

Publications

Chen T,Gupta A, Zalavadia M, Streets A. “µCB-seq: Microfluidic cell barcoding and sequencing for high-resolution imaging and sequencing of single cells” Lab Chip, 2020, 20, 3899-3913. DOI: 10.109/D0LC00169D

Related Web Links

http://streetslab.berkeley.edu/

Keywords

Fluorescence, Genetic Dissection, Microfluidics, scRNAseq, Single cell, Single cell analysis, single cell genomics, single cell RNA sequencing, single cell transcriptomics

Reference

Chan Zuckerberg ref. CZB-133B, Berkeley ref. B19-175