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Abstract
Epigenome regulation has emerged as an important mechanism for the maintenance of organ function in health and disease. Dissecting epigenomic alterations and resultant gene expression changes in single cells provides unprecedented resolution and insight into cellular diversity, modes of gene regulation, transcription factor dynamics and 3D genome organization. In this chapter, we summarize the transformative single-cell epigenomic technologies that have deepened our understanding of the fundamental principles of gene regulation. We provide a historical perspective of these methods, brief procedural outline with emphasis on the computational tools used to meaningfully dissect information. Our overall goal is to aid scientists using these technologies in their favorite system of interest.
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Affiliation(s)
- Krystyna Mazan-Mamczarz
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Jisu Ha
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
- Laboratory of Genetics and Genomics, and Computational Biology and Genomics Core, National Institute on Aging-Intramural Research Program, National Institute of Health, Baltimore, MD, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA.
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McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, Chow ED, Gartner ZJ. MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. Nat Methods 2019. [PMID: 31209384 DOI: 10.1101/387241] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
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.
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Affiliation(s)
- Christopher S McGinnis
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David M Patterson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Juliane Winkler
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Daniel N Conrad
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Marco Y Hein
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Vasudha Srivastava
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer L Hu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Lyndsay M Murrow
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Zena Werb
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Center for Advanced Technology, University of California San Francisco, San Francisco, CA, USA.
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.
- Chan Zuckerberg BioHub, University of California San Francisco, San Francisco, CA, USA.
- Center for Cellular Construction, University of California San Francisco, San Francisco, CA, USA.
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Guo C, Kong W, Kamimoto K, Rivera-Gonzalez GC, Yang X, Kirita Y, Morris SA. CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics. Genome Biol 2019; 20:90. [PMID: 31072405 PMCID: PMC6509836 DOI: 10.1186/s13059-019-1699-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 04/23/2019] [Indexed: 12/15/2022] Open
Abstract
High-throughput single-cell assays increasingly require special consideration in experimental design, sample multiplexing, batch effect removal, and data interpretation. Here, we describe a lentiviral barcode-based multiplexing approach, CellTag Indexing, which uses predefined genetic barcodes that are heritable, enabling cell populations to be tagged, pooled, and tracked over time in the same experimental replicate. We demonstrate the utility of CellTag Indexing by sequencing transcriptomes using a variety of cell types, including long-term tracking of cell engraftment and differentiation in vivo. Together, this presents CellTag Indexing as a broadly applicable genetic multiplexing tool that is complementary with existing single-cell technologies.
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Affiliation(s)
- Chuner Guo
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Wenjun Kong
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Guillermo C Rivera-Gonzalez
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Xue Yang
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Yuhei Kirita
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Division of Nephrology, Department of Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA.
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA.
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA.
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Guo C, Kong W, Kamimoto K, Rivera-Gonzalez GC, Yang X, Kirita Y, Morris SA. CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics. Genome Biol 2019. [PMID: 31072405 DOI: 10.1101/335547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
High-throughput single-cell assays increasingly require special consideration in experimental design, sample multiplexing, batch effect removal, and data interpretation. Here, we describe a lentiviral barcode-based multiplexing approach, CellTag Indexing, which uses predefined genetic barcodes that are heritable, enabling cell populations to be tagged, pooled, and tracked over time in the same experimental replicate. We demonstrate the utility of CellTag Indexing by sequencing transcriptomes using a variety of cell types, including long-term tracking of cell engraftment and differentiation in vivo. Together, this presents CellTag Indexing as a broadly applicable genetic multiplexing tool that is complementary with existing single-cell technologies.
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Affiliation(s)
- Chuner Guo
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Wenjun Kong
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Guillermo C Rivera-Gonzalez
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Xue Yang
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Yuhei Kirita
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
- Division of Nephrology, Department of Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine in St Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA.
- Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA.
- Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO, 63110, USA.
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McGinnis CS, Murrow LM, Gartner ZJ. DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors. Cell Syst 2019; 8:329-337.e4. [PMID: 30954475 DOI: 10.1101/352484] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 11/15/2018] [Accepted: 03/06/2019] [Indexed: 05/24/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) data are commonly affected by technical artifacts known as "doublets," which limit cell throughput and lead to spurious biological conclusions. Here, we present a computational doublet detection tool-DoubletFinder-that identifies doublets using only gene expression data. DoubletFinder predicts doublets according to each real cell's proximity in gene expression space to artificial doublets created by averaging the transcriptional profile of randomly chosen cell pairs. We first use scRNA-seq datasets where the identity of doublets is known to show that DoubletFinder identifies doublets formed from transcriptionally distinct cells. When these doublets are removed, the identification of differentially expressed genes is enhanced. Second, we provide a method for estimating DoubletFinder input parameters, allowing its application across scRNA-seq datasets with diverse distributions of cell types. Lastly, we present "best practices" for DoubletFinder applications and illustrate that DoubletFinder is insensitive to an experimentally validated kidney cell type with "hybrid" expression features.
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Affiliation(s)
- Christopher S McGinnis
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Lyndsay M Murrow
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerbeg Biohub, University of California, San Francisco, San Francisco, CA, USA; Center for Cellular Construction, University of California, San Francisco, San Francisco, CA, USA.
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