학술논문
Microfluidics-free single-cell genomics with templated emulsification
Document Type
Original Paper
Author
Clark, Iain C.; Fontanez, Kristina M.; Meltzer, Robert H.; Xue, Yi; Hayford, Corey; May-Zhang, Aaron; D’Amato, Chris; Osman, Ahmad; Zhang, Jesse Q.; Hettige, Pabodha; Ishibashi, Jacob S. A.; Delley, Cyrille L.; Weisgerber, Daniel W.; Replogle, Joseph M.; Jost, Marco; Phong, Kiet T.; Kennedy, Vanessa E.; Peretz, Cheryl A. C.; Kim, Esther A.; Song, Siyou; Karlon, William; Weissman, Jonathan S.; Smith, Catherine C.; Gartner, Zev J.; Abate, Adam R.
Source
Nature Biotechnology: The Science and Business of Biotechnology. 41(11):1557-1566
Subject
Language
English
ISSN
1087-0156
1546-1696
1546-1696
Abstract
Current single-cell RNA-sequencing approaches have limitations that stem from the microfluidic devices or fluid handling steps required for sample processing. We develop a method that does not require specialized microfluidic devices, expertise or hardware. Our approach is based on particle-templated emulsification, which allows single-cell encapsulation and barcoding of cDNA in uniform droplet emulsions with only a vortexer. Particle-templated instant partition sequencing (PIP-seq) accommodates a wide range of emulsification formats, including microwell plates and large-volume conical tubes, enabling thousands of samples or millions of cells to be processed in minutes. We demonstrate that PIP-seq produces high-purity transcriptomes in mouse–human mixing studies, is compatible with multiomics measurements and can accurately characterize cell types in human breast tissue compared to a commercial microfluidic platform. Single-cell transcriptional profiling of mixed phenotype acute leukemia using PIP-seq reveals the emergence of heterogeneity within chemotherapy-resistant cell subsets that were hidden by standard immunophenotyping. PIP-seq is a simple, flexible and scalable next-generation workflow that extends single-cell sequencing to new applications.
A microfluidics-free, scalable single-cell RNA-sequencing method produces high-quality transcriptomes.
A microfluidics-free, scalable single-cell RNA-sequencing method produces high-quality transcriptomes.