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Nat Methods. 2019 Jul;16(7):619-626. doi: 10.1038/s41592-019-0433-8. Epub 2019 Jun 17.

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices.

Author information

1
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
2
Department of Anatomy, University of California San Francisco, San Francisco, CA, USA.
3
Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
4
Howard Hughes Medical Institute, Chevy Chase, MD, USA.
5
Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.
6
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA. eric.chow@ucsf.edu.
7
Center for Advanced Technology, University of California San Francisco, San Francisco, CA, USA. eric.chow@ucsf.edu.
8
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA. zev.gartner@ucsf.edu.
9
Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA. zev.gartner@ucsf.edu.
10
Chan Zuckerberg BioHub, University of California San Francisco, San Francisco, CA, USA. zev.gartner@ucsf.edu.
11
Center for Cellular Construction, University of California San Francisco, San Francisco, CA, USA. zev.gartner@ucsf.edu.

Abstract

Sample multiplexing facilitates scRNA-seq by reducing costs and identifying artifacts such as cell doublets. However, universal and scalable sample barcoding strategies have not been described. We therefore developed MULTI-seq: multiplexing using lipid-tagged indices for single-cell and single-nucleus RNA sequencing. MULTI-seq reagents can barcode any cell type or nucleus from any species with an accessible plasma membrane. The method involves minimal sample processing, thereby preserving cell viability and endogenous gene expression patterns. When cells are classified into sample groups using MULTI-seq barcode abundances, data quality is improved through doublet identification and recovery of cells with low RNA content that would otherwise be discarded by standard quality-control workflows. We use MULTI-seq to track the dynamics of T-cell activation, perform a 96-plex perturbation experiment with primary human mammary epithelial cells and multiplex cryopreserved tumors and metastatic sites isolated from a patient-derived xenograft mouse model of triple-negative breast cancer.

PMID:
31209384
DOI:
10.1038/s41592-019-0433-8
[Indexed for MEDLINE]

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