PUBLICATION
Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars
- Authors
- Spanjaard, B., Hu, B., Mitic, N., Olivares-Chauvet, P., Janjuha, S., Ninov, N., Junker, J.P.
- ID
- ZDB-PUB-180418-26
- Date
- 2018
- Source
- Nature Biotechnology 36(5): 469-473 (Journal)
- Registered Authors
- Ninov, Nikolay
- Keywords
- none
- Datasets
- 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.
Citation
Spanjaard, B., Hu, B., Mitic, N., Olivares-Chauvet, P., Janjuha, S., Ninov, N., Junker, J.P. (2018) Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars. Nature Biotechnology. 36(5):469-473.
Abstract
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping