1. Microfluidics-free single-cell genomics with templated emulsification
- Author
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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 SA, Delley, Cyrille L, Weisgerber, Daniel W, Replogle, Joseph M, Jost, Marco, Phong, Kiet T, Kennedy, Vanessa E, Peretz, Cheryl AC, Kim, Esther A, Song, Siyou, Karlon, William, Weissman, Jonathan S, Smith, Catherine C, Gartner, Zev J, and Abate, Adam R
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,Bioengineering ,Human Genome ,Humans ,Animals ,Mice ,Microfluidics ,High-Throughput Nucleotide Sequencing ,Single-Cell Analysis ,Genomics ,Transcriptome - 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.
- Published
- 2023