CellDestiny: A RShiny application for the visualization and analysis of single-cell lineage tracing data

Single-cell lineage tracing permits the labeling of individual cells with a heritable marker to follow the fate of each cell’s progeny. Over the last twenty years, several single-cell lineage tracing methods have emerged, enabling major discoveries in developmental biology, oncology and gene therapi...

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Vydané v:Frontiers in medicine Ročník 9; s. 919345
Hlavní autori: Hadj Abed, Louisa, Tak, Tamar, Cosgrove, Jason, Perié, Leïla
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: Switzerland Frontiers Media SA 05.10.2022
Frontiers media
Frontiers Media S.A
Predmet:
Bar codes
Bioengineering
bioinformatics
Biologists
Biology
Cellular Biology
Cloning
Data analysis
Datasets
gene therapy
Labeling
lentiviral barcoding
Life Sciences
lineage tracing
Medicine
Metadata
Quality control
single-cell
Software
Statistical analysis
Subcellular Processes
Visualization
lentiviral barcoding
single-cell
gene therapy
data analysis
lineage tracing
bioinformatics
ISSN:2296-858X, 2296-858X
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Popis
Shrnutí:Single-cell lineage tracing permits the labeling of individual cells with a heritable marker to follow the fate of each cell’s progeny. Over the last twenty years, several single-cell lineage tracing methods have emerged, enabling major discoveries in developmental biology, oncology and gene therapies. Analytical tools are needed to draw meaningful conclusions from lineage tracing measurements, which are characterized by high variability, sparsity and technical noise. However, the single cell lineage tracing field lacks versatile and easy-to-use tools for standardized and reproducible analyses, in particular tools accessible to biologists. Here we present CellDestiny, a RShiny app and associated web application developed for experimentalists without coding skills to perform visualization and analysis of single cell lineage-tracing datasets through a graphical user interface. We demonstrate the functionality of CellDestiny through the analysis of (i) lentiviral barcoding datasets of murine hematopoietic progenitors; (ii) published integration site data from Wiskott-Aldrich Symdrome patients undergoing gene-therapy treatment; and (iii) simultaneous barcoding and transcriptomic analysis of murine hematopoietic progenitor differentiation in vitro . In summary, CellDestiny is an easy-to-use and versatile toolkit that enables biologists to visualize and analyze single-cell lineage tracing data.
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This article was submitted to Gene and Cell Therapy, a section of the journal Frontiers in Medicine
Reviewed by: Lars Thielecke, Technical University Dresden, Germany; Jinzhuang Dou, The University of Texas MD Anderson Cancer Center, United States; Mark Enstrom, Fred Hutchinson Cancer Research Center, United States
Edited by: Ingmar Glauche, Technical University Dresden, Germany
ISSN:2296-858X
2296-858X
DOI:10.3389/fmed.2022.919345