title: Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding.
abstract: Lineage tracing by the determination and mapping of progeny arising from single cells is an important approach enabling the elucidation of mechanisms underlying diverse biological processes ranging from development to disease. We developed a dynamic sequence-based barcode system for synthetic lineage tracing and have demonstrated its performance in C. elegans, a model organism whose lineage tree is well established. The strategy we use creates lineage trees based upon the introduction of synthetically controlled mutations into cells and the propagation of these mutations to daughter cells at each cell division. We analyzed this experimental proof of concept along with a corresponding simulation and analytical model to gain a deeper understanding of the coding capacity of the system. Our results provide specific bounds on the fidelity of lineage tracing using such approaches.
authors.affiliation: Department of Bioengineering, Stanford University , Stanford, California 94305, United States.
authors.forename: Stephanie Tzouanas
authors.identifier: 0000-0003-3560-5782
authors.initials: ST
authors.lastname: Schmidt
authors.affiliation: Department of Genetics, Stanford University , Stanford, California 94305, United States.
authors.forename: Stephanie M
authors.initials: SM
authors.lastname: Zimmerman
authors.affiliation: Department of Bioengineering, Stanford University , Stanford, California 94305, United States.
authors.forename: Jianbin
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Genetics, Stanford University , Stanford, California 94305, United States.|Department of Developmental Biology, Stanford University , Stanford, California 94305, United States.
authors.forename: Stuart K
authors.initials: SK
authors.lastname: Kim
authors.affiliation: Department of Bioengineering, Stanford University , Stanford, California 94305, United States.|Department of Applied Physics, Stanford University , Stanford, California 94305, United States.|Chan Zuckerberg Biohub , San Francisco, California 94518, United States.
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Quake
mesh_terms: D000818:Animals; D064113:CRISPR-Cas Systems / Q000235:genetics; D017173:Caenorhabditis elegans / Q000145:classification / Q000235:genetics; D019070:Cell Lineage / Q000235:genetics*; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D018509:DNA, Helminth / Q000235:genetics; D054643:INDEL Mutation / Q000235:genetics; D008957:Models, Genetic; D058615:Synthetic Biology / Q000379:methods*
chemical_list: D018509:DNA, Helminth
keywords: CRISPR/Cas9; DNA barcoding; lineage tracing