Rapid microfluidic isolation of virally infected primary bronchial epithelial cells for single-cell RNA sequencing

Single-cell RNA sequencing (scRNA-seq) of the bronchial epithelium enables examination of cellular subtypes and their responses to viral infections. Researchers from the University of Southampton have developed an optimized method for the isolation of virally infected primary bronchial epithelial cells using a commercially available microfluidic device. Using this method single cells can be rapidly isolated with minimal equipment available in most laboratories. Isolation can be carried out inside biological safety cabinets, permitting the use of virally infected cells. Both cell-line and primary cells isolated using the device retained sufficient RNA integrity for the generation of short-read sequencing-compatible cDNA libraries to facilitate scRNA-seq.

Smart Aliquotor CE device and workflow

(A) Workflow of the single-cell isolation process ending with an isolated single cell. (B) Smart Aliquotor CE device. (C) A single primary bronchial epithelial cell (PBEC) (red box) in a well of the device. (D) Three PBECs (red boxes) in a well of the device. (E) Two human esophageal adenocarcinoma (FLO1) cells labeled with CFSE in a well of the device. (F) Transfer of a single cell from a well of the device to a slide; droplet contains a single cell (red box showing the single cell at ×20 magnification).

Kimbley LM, Parker R, Jongen MS, Holloway JW, Swindle EJ, Rose-Zerilli MJJ. (2021) Rapid microfluidic isolation of virally infected primary bronchial epithelial cells for single-cell RNA sequencing. Biotechniques [Epub ahead of print]. [abstract]

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