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Decoding cell division history and lineage-resolved phenotypic patterns from single-cell barcode and transcriptomic data

Identification

Clé publique

radar:r-18ec2e5199fd3970757047fc28fba434

Auteurs

Xiaochen Yu · Zihao Wang · Zhenquan Zhang · Yuxin Wang · Yuting Lin · L. Elliot Hong · Xiaoshu Chen · Xionglei He · Jian‐Rong Yang · Jiajun Zhang

Année déclarée

2026

Langue déclarée

en

Type source

preprint

Première détection

2026-11-14T02:13:03.394657+00:00

Dernière observation des métadonnées

2026-11-14T02:13:03.394657+00:00

Dernière vérification HTTP

Non effectuée

Institutions déclarées par la source

Sun Yat-sen University · Guangdong University of Technology · Guangdong Province Key Laboratory of Computational Science

Pays d’affiliation déclarés

CN

Résumé documentaire — langue originale

The cell division tree encodes how proliferation and differentiation generate cellular diversity during multicellular development. Advances in single-cell RNA sequencing and CRISPR-based lineage tracing have enabled retrospective reconstruction of these histories at single-cell resolution. Here, we present FateScape, a statistical framework that integrates paired lineage barcodes and transcriptomic profiles to infer cell division topology and characterize depth-resolved phenotypic patterns. FateScape combines barcode consistency with transcriptome-derived state continuity through overlapping state-lineage decomposition and barcode-guided subtree integration. Here, to analyze phenotypic patterns on the inferred tree, we introduce entropy paths, which measure how cells of each state are distributed across depth-defined subtrees, and Moran's I –derived statistics for same-state autocorrelation and cross-state association. In simulations, FateScape shows robust reconstruction performance across varying mutation rates, dropout levels, sample sizes, and barcode target-site numbers. In the Caenorhabditis elegans data analysis, FateScape accurately recovers lineage topology and identifies depth-resolved state patterns, including concentrated intestinal cells and broadly distributed neuronal and glial states. In mouse embryos, FateScape quantifies distinct germ-layer patterns, including early endodermal concentration, broad ectodermal distribution across shallow-to-intermediate depths, and intermediate mesodermal distribution followed by deeper concentration. Together, FateScape provides a framework for reconstructing cell division histories and quantifying state dispersion, concentration, and tree-based association across lineage depth.

Identifiants

OPENALEX

https://openalex.org/W7213871437

DOI

10.1101/gr.281734.125

PMID

https://pubmed.ncbi.nlm.nih.gov/42767804

Repères documentaires

Famille documentaire

preprint

Types déclarés par les sources

preprint

Éditeurs

Cold Spring Harbor Laboratory Press

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Sources

OpenAlex · Document 1

• Document · https://doi.org/10.1101/gr.281734.125

Statut documentaire

Pertinence à examiner

Bibliothèque

Cette identité n’est pas encore intégrée à la Bibliothèque juridique.