Lineage Tracing Methods and Protocols

This volume covers the state-of-art lineage tracing methods, to record these recent multi-front rapid progresses and promote development of further powerful tools. Chapters explores a broad spectrum of techniques that have been developed and refined over the years, offering a detailed exposition of their principles, applications, and limitations. Additional chapters cover classic methods, such as genetic lineage tracing, clonal analysis, single-cell RNA sequencing, and live-cell imaging. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Lineage Tracing: Methods and Protocols aims to serve as a valuable resource, fostering new discoveries and advancements in the exciting field of cell lineage tracing.

Bayesian Phylogenetic Lineage Reconstruction with Loss of Heterozygosity Mutations Derived from Single-cell RNA Sequencing.- Tracking somatic mutations for lineage reconstruction.- Multicolor cell lineage tracing using MAGIC Markers strategies.- Single cell lineage tracing and clonal state-fate analysis.- Lineage recording in human brain organoids with iTracer.- Clonal tracking in the mouse brain with single-cell RNA-seq.- Lineage tracing by light-sheet microscopy and computational reconstruction.- Reconstructing progenitor state hierarchy and dynamics using lineage barcoding data.- Tracking cell phylogenies in the human brain with somatic mosaic mutations.- Paired single-cell transcriptome and DNA barcode detection in zebrafish using ScarTrace.- LINNAEUS - Simultaneous single-cell lineage tracing and cell type identification.- In Vivo Clonal Analysis Using MADM with Spatio-temporal Specificity.- CARLIN: a mouse line for simultaneous readout of lineage histories and gene expression.- Single-cell profiling of lineages and cell types in the vertebrate brain.- StarTrack: Mapping Cellular Fates with Inheritable Color Codes.- Design and generation of TEMPO reagents for sequential labelling and manipulation of vertebrate cell lineages.- Computational Methods for Lineage Reconstruction.- GEMLI: Gene expression memory-based lineage inference from single cell RNA-sequencing datasets.- Lineage analysis at single-cell resolution by twin-spot MARCM with lineage-restricted drivers.- CLADES: a programmable cascade of genes for cell lineage analysis and manipulation.