CellTagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution.,Nature Protocols

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CellTagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution.
Nature Protocols ( IF 13.1 ) Pub Date : 2020-02-12 , DOI: 10.1038/s41596-019-0247-2
Wenjun Kong _{1,

2,

3} , Brent A Biddy _{1,

2,

3} , Kenji Kamimoto _{1,

2,

3} , Junedh M Amrute _{1,

2,

3} , Emily G Butka _{1,

2,

3} , Samantha A Morris _{1,

2,

3}

Affiliation

Single-cell technologies are offering unparalleled insight into complex biology, revealing the behavior of rare cell populations that are masked in bulk population analyses. One current limitation of single-cell approaches is that lineage relationships are typically lost as a result of cell processing. We recently established a method, CellTagging, permitting the parallel capture of lineage information and cell identity via a combinatorial cell indexing approach. CellTagging integrates with high-throughput single-cell RNA sequencing, where sequential rounds of cell labeling enable the construction of multi-level lineage trees. Here, we provide a detailed protocol to (i) generate complex plasmid and lentivirus CellTag libraries for labeling of cells; (ii) sequentially CellTag cells over the course of a biological process; (iii) profile single-cell transcriptomes via high-throughput droplet-based platforms; and (iv) generate a CellTag expression matrix, followed by clone calling and lineage reconstruction. This lentiviral-labeling approach can be deployed in any organism or in vitro culture system that is amenable to viral transduction to simultaneously profile lineage and identity at single-cell resolution.

中文翻译：

CellTagging：组合索引，以单细胞分辨率同时映射谱系和身份。

单细胞技术为复杂生物学提供了无与伦比的洞察力，揭示了在大批种群分析中掩盖的稀有细胞种群的行为。单细胞方法的当前局限性是谱系关系通常由于细胞处理而丢失。我们最近建立了一种方法，即CellTagging，它允许通过组合细胞索引方法并行捕获谱系信息和细胞身份。CellTagging与高通量单细胞RNA测序集成在一起，在此过程中，连续的细胞标记循环可构建多级谱系树。在这里，我们提供了详细的协议（i）生成用于质粒标记的复杂质粒和慢病毒CellTag库；（ii）在生物过程中依次使用CellTag细胞；（iii）通过基于高通量液滴的平台分析单细胞转录组；（iv）生成CellTag表达矩阵，然后进行克隆调用和谱系重建。这种慢病毒标记方法可以部署在任何适合于病毒转导的生物体或体外培养系统中，从而以单细胞分辨率同时分析谱系和特性。

更新日期：2020-02-12

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