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URL: https://dx.doi.org/10.17504/protocols.io.yxifxke

Authors: Brent A. Biddy, Wenjun Kong, Kenji Kamimoto, Chuner Guo, Sarah Waye, Tao Sun, Samantha Morris

Group: Human Cell Atlas Method Development Community, Morris Lab

Summary: Single-cell technologies are offering unprecedented insight into complex biology, revealing the behavior of rare cell populations that are typically masked in bulk population analyses. One current limitation of single-cell approaches is that lineage relationships are lost as a result of cell processing, restricting interpretations of the data collected. Elegant computational approaches have been developed in an effort to infer these missing observations, but it remains a challenge to reconstruct true reprogramming trajectories using these tools. Although sophisticated lineage tracing solutions to connect cell history with fate are emerging, these protocols are either not compatible with high-throughput scRNA-seq, or require genome editing strategies that are not readily deployed in some systems. Here, our protocol describes a single-cell resolution clonal tracking approach, ‘CellTagging’, based on combinatorial cell indexing, permitting the parallel capture of lineage information and cell identity. CellTagging integrates with high-throughput single-cell RNA-sequencing, where iterative rounds of cell labeling enable the construction of multi-level lineage trees. This straightforward lentiviral-labeling approach can be applied to an array of cell biological applications to simultaneously profile lineage and identity, at single-cell resolution.

Affiliations: Department of Developmental Biology; Department of Genetics; Center of Regenerative Medicine. Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA., Department of Developmental Biology; Department of Genetics; Center of Regenerative Medicine. Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA., Department of Developmental Biology; Department of Genetics; Center of Regenerative Medicine. Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA., Department of Developmental Biology; Department of Genetics; Center of Regenerative Medicine. Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA., Department of Developmental Biology; Department of Genetics; Center of Regenerative Medicine. Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA., Department of Developmental Biology; Department of Genetics; Center of Regenerative Medicine. Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA., Department of Developmental Biology; Department of Genetics; Center of Regenerative Medicine. Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA.

Version: 8

Publication Date: 2019

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