There is a growing interest in developing experimental methods for tracking the developmental cell lineages of a complex organism. The recently developed CRISPR/Cas9-based barcoding method is, although highly promising, difficult to scale up because it relies on exogenous barcoding sequences that are engineered into the genome. In this study, we characterized 78 high-quality endogenous sites in the zebrafish genome that can be used as CRISPR/Cas9-based barcoding sites. The 78 sites are all highly expressed in most of the cell types according to single-cell RNA sequencing (scRNA-seq) data. Hence, the barcoding information of the 78 endogenous sites is recovered by the available scRNA-seq platforms, enabling simultaneous characterization of cell type and cell lineage information.

对开发用于追踪复杂生物的发育细胞谱系的实验方法的兴趣日益增长。最近开发的基于CRISPR / Cas9的条形码技术尽管很有希望，但由于其依赖于基因组中工程化的外源条形码序列，因此很难扩大规模。在这项研究中，我们表征了斑马鱼基因组中的78个高质量内源性位点，这些位点可用作基于CRISPR / Cas9的条形码位点。根据单细胞RNA测序（scRNA-seq）数据，这78个位点在大多数细胞类型中均高表达。因此，可通过可用的scRNA-seq平台恢复78个内源位点的条形码信息，从而能够同时表征细胞类型和细胞谱系信息。