CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics

被引：55
作者：
Guo, Chuner [1 ,2 ,3 ]
Kong, Wenjun [1 ,2 ,3 ]
Kamimoto, Kenji [1 ,2 ,3 ]
Rivera-Gonzalez, Guillermo C. [1 ,2 ,3 ]
Yang, Xue [1 ,2 ,3 ]
Kirita, Yuhei [2 ,4 ]
Morris, Samantha A. [1 ,2 ,3 ]
机构：
[1] Washington Univ, Dept Dev Biol, Sch Med St Louis, 660 S Euclid Ave,Campus Box 8103, St Louis, MO 63110 USA
[2] Washington Univ, Dept Genet, Sch Med St Louis, 660 S Euclid Ave,Campus Box 8103, St Louis, MO 63110 USA
[3] Washington Univ, Ctr Regenerat Med, Sch Med St Louis, 660 S Euclid Ave,Campus Box 8103, St Louis, MO 63110 USA
[4] Washington Univ, Div Nephrol, Dept Med, Sch Med St Louis, 660 S Euclid Ave,Campus Box 8103, St Louis, MO 63110 USA
来源：
GENOME BIOLOGY | 2019年 / 20卷 / 1期
基金：
美国国家卫生研究院; 日本学术振兴会;
关键词：
STEM-CELLS; NEGATIVE REGULATOR; EXPRESSION; LRIG1; MARKER; IDENTITY; FATE; CONVERSION; LINEAGES; CIRCUITS;
D O I：
10.1186/s13059-019-1699-y
中图分类号：
Q81 [生物工程学（生物技术）]; Q93 [微生物学];
学科分类号：
071005 ; 0836 ; 090102 ; 100705 ;
摘要：
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.
引用
收藏
页数：13
相关论文
共 57 条
[1]   A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response [J].
Adamson, Britt ;
Norman, Thomas M. ;
Jost, Marco ;
Cho, Min Y. ;
Nunez, James K. ;
Chen, Yuwen ;
Villalta, Jacqueline E. ;
Gilbert, Luke A. ;
Horlbeck, Max A. ;
Hein, Marco Y. ;
Pak, Ryan A. ;
Gray, Andrew N. ;
Gross, Carol A. ;
Dixit, Atray ;
Parnas, Oren ;
Regev, Aviv ;
Weissman, Jonathan S. .
CELL, 2016, 167 (07) :1867-+
[2]   Identification of stem cells in small intestine and colon by marker gene Lgr5 [J].
Barker, Nick ;
van Es, Johan H. ;
Kuipers, Jeroen ;
Kujala, Pekka ;
van den Born, Maaike ;
Cozijnsen, Miranda ;
Haegebarth, Andrea ;
Korving, Jeroen ;
Begthel, Harry ;
Peters, Peter J. ;
Clevers, Hans .
NATURE, 2007, 449 (7165) :1003-U1
[3]   Dimensionality reduction for visualizing single-cell data using UMAP [J].
Becht, Etienne ;
McInnes, Leland ;
Healy, John ;
Dutertre, Charles-Antoine ;
Kwok, Immanuel W. H. ;
Ng, Lai Guan ;
Ginhoux, Florent ;
Newell, Evan W. .
NATURE BIOTECHNOLOGY, 2019, 37 (01) :38-+
[4]   Single-cell mapping of lineage and identity in direct reprogramming [J].
Biddy, Brent A. ;
Kong, Wenjun ;
Kamimoto, Kenji ;
Guo, Chuner ;
Waye, Sarah E. ;
Sun, Tao ;
Morris, Samantha A. .
NATURE, 2018, 564 (7735) :219-+
[5]   Epidermolysis bullosa and embryonic lethality in mice lacking the multi-PDZ domain protein GRIP1 [J].
Bladt, F ;
Tafuri, A ;
Gelkop, S ;
Langille, L ;
Pawson, T .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (10) :6816-6821
[6]   A Robust and Highly Efficient Immune Cell Reprogramming System [J].
Bussmann, Lars H. ;
Schubert, Alexis ;
Vu Manh, Thien Phong ;
De Andres, Luisa ;
Desbordes, Sabrina C. ;
Parra, Maribel ;
Zimmermann, Timo ;
Rapino, Francesca ;
Rodriguez-Ubreva, Javier ;
Ballestar, Esteban ;
Graf, Thomas .
CELL STEM CELL, 2009, 5 (05) :554-566
[7]   Integrating single-cell transcriptomic data across different conditions, technologies, and species [J].
Butler, Andrew ;
Hoffman, Paul ;
Smibert, Peter ;
Papalexi, Efthymia ;
Satija, Rahul .
NATURE BIOTECHNOLOGY, 2018, 36 (05) :411-+
[8]   Comprehensive single-cell transcriptional profiling of a multicellular organism [J].
Cao, Junyue ;
Packer, Jonathan S. ;
Ramani, Vijay ;
Cusanovich, Darren A. ;
Huynh, Chau ;
Daza, Riza ;
Qiu, Xiaojie ;
Lee, Choli ;
Furlan, Scott N. ;
Steemers, Frank J. ;
Adey, Andrew ;
Waterston, Robert H. ;
Trapnell, Cole ;
Shendure, Jay .
SCIENCE, 2017, 357 (6352) :661-667
[9]   Gastrointestinal differentiation marker Cytokeratin 20 is regulated by homeobox gene CDX1 [J].
Chan, Carol W. M. ;
Wong, Newton A. ;
Liu, Ying ;
Bicknell, David ;
Turley, Helen ;
Hollins, Laura ;
Miller, Crispin J. ;
Wilding, Jennifer L. ;
Bodmer, Walter F. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (06) :1936-1941
[10]  
Datlinger P, 2017, NAT METHODS, V14, P297, DOI [10.1038/NMETH.4177, 10.1038/nmeth.4177]
123456