TY - CHAP
T1 - Reconstructing Progenitor State Hierarchy and Dynamics Using Lineage Barcoding Data
AU - Fang, Weixiang
AU - Yang, Yi
AU - Ji, Hongkai
AU - Kalhor, Reza
N1 - Publisher Copyright:
© The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2025.
PY - 2025
Y1 - 2025
N2 - Measurements of cell phylogeny based on natural or induced mutations, known as lineage barcodes, in conjunction with molecular phenotype have become increasingly feasible for a large number of single cells. In this chapter, we delve into Quantitative Fate Mapping (QFM) and its computational pipeline, which enables the interrogation of the dynamics of progenitor cells and their fate restriction during development. The methods described here include inferring cell phylogeny with the Phylotime model, and reconstructing progenitor state hierarchy, commitment time, population size, and commitment bias with the ICE-FASE algorithm. Evaluation of adequate sampling based on progenitor state coverage statistics is emphasized for interpreting the QFM results. Overall, this chapter describes a general framework for characterizing the dynamics of cell fate changes using lineage barcoding data.
AB - Measurements of cell phylogeny based on natural or induced mutations, known as lineage barcodes, in conjunction with molecular phenotype have become increasingly feasible for a large number of single cells. In this chapter, we delve into Quantitative Fate Mapping (QFM) and its computational pipeline, which enables the interrogation of the dynamics of progenitor cells and their fate restriction during development. The methods described here include inferring cell phylogeny with the Phylotime model, and reconstructing progenitor state hierarchy, commitment time, population size, and commitment bias with the ICE-FASE algorithm. Evaluation of adequate sampling based on progenitor state coverage statistics is emphasized for interpreting the QFM results. Overall, this chapter describes a general framework for characterizing the dynamics of cell fate changes using lineage barcoding data.
KW - ICE-FASE
KW - Lineage barcoding pipeline
KW - Lineage tracing
KW - Phylotime
KW - Progenitor state dynamics
KW - Quantitative fate mapping (QFM)
KW - Time-scaled cell phylogeny
UR - http://www.scopus.com/inward/record.url?scp=85214330151&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85214330151&partnerID=8YFLogxK
U2 - 10.1007/978-1-0716-4310-5_9
DO - 10.1007/978-1-0716-4310-5_9
M3 - Chapter
C2 - 39745641
AN - SCOPUS:85214330151
T3 - Methods in Molecular Biology
SP - 177
EP - 199
BT - Methods in Molecular Biology
PB - Humana Press Inc.
ER -