LINNAEUS: simultaneous single-cell lineage tracing and cell type identification

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Item Type:	Article
Title:	LINNAEUS: simultaneous single-cell lineage tracing and cell type identification
Creators Name:	Spanjaard, B. and Junker, J.P.
Abstract:	A key goal of biology is to understand the origin of the many cell types that can be observed during diverse processes such as development, regeneration, and disease. 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 origins of cell states and relationships between cells remains challenging. Here we present LINNAEUS (Spanjaard et al, Nat Biotechnol 36:469–473. https://doi.org/10.1038/nbt.4124, 2018; Hu et al, Nat Genet 54:1227–1237. https://doi.org/10.1038/s41588-022-01129-5, 2022) (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, LINNAEUS can be used to reconstruct organism-wide single-cell lineage trees. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.
Keywords:	Single-Cell MRNA, Single-Cell Lineage Tracing, Barcoding, CRISPR/Cas9, Tree Building, Phylogenetics, Animals
Source:	Methods in Molecular Biology
Series Name:	Methods in Molecular Biology
Title of Book:	Lineage Tracing
ISSN:	1064-3745
ISBN:	978-1-0716-4309-9
Publisher:	Springer / Humana Press
Volume:	2886
Page Range:	243-263
Date:	3 January 2025
Official Publication:	https://doi.org/10.1007/978-1-0716-4310-5_12
PubMed:	View item in PubMed

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