ZFIN ID: ZDB-PUB-180418-26
Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars
Spanjaard, B., Hu, B., Mitic, N., Olivares-Chauvet, P., Janjuha, S., Ninov, N., Junker, J.P.
Date: 2018
Source: Nature Biotechnology   36(5): 469-473 (Journal)
Registered Authors: Ninov, Nikolay
Keywords: none
Microarrays: GEO:GSE106121
MeSH Terms:
  • Animals
  • CRISPR-Cas Systems/genetics*
  • Cell Lineage/genetics
  • Cell Tracking/methods
  • Computational Biology/methods
  • Gene Editing*
  • Genetic Engineering
  • Heart/growth & development
  • High-Throughput Nucleotide Sequencing/methods
  • Liver/growth & development
  • Liver/metabolism
  • Pancreas/growth & development
  • Pancreas/metabolism
  • Single-Cell Analysis/methods
  • Telencephalon/growth & development
  • Telencephalon/metabolism
  • Transcriptome/genetics*
  • Zebrafish/genetics*
  • Zebrafish/growth & development
  • Zebrafish/metabolism
PubMed: 29644996 Full text @ Nat Biotechnol.
A key goal of developmental biology is to understand how a single cell is transformed into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the developmental origin of cells remains challenging. Here we present LINNAEUS (lineage tracing by nuclease-activated editing of ubiquitous sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae, and in heart, liver, pancreas, and telencephalon of adult fish. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.