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Trajectories of Cell-cycle Progression from Fixed Cell Populations

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Journal Nat Methods
Date 2015 Aug 25
PMID 26301842
Citations 51
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Abstract

An accurate dissection of sources of cell-to-cell variability is crucial for quantitative biology at the single-cell level but has been challenging for the cell cycle. We present Cycler, a robust method that constructs a continuous trajectory of cell-cycle progression from images of fixed cells. Cycler handles heterogeneous microenvironments and does not require perturbations or genetic markers, making it generally applicable to quantifying multiple sources of cell-to-cell variability in mammalian cells.

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References
1.
Bendall S, Davis K, Amir E, Tadmor M, Simonds E, Chen T . Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell. 2014; 157(3):714-25. PMC: 4045247. DOI: 10.1016/j.cell.2014.04.005. View

2.
Eldar A, Elowitz M . Functional roles for noise in genetic circuits. Nature. 2010; 467(7312):167-73. PMC: 4100692. DOI: 10.1038/nature09326. View

3.
Carpenter A, Jones T, Lamprecht M, Clarke C, Kang I, Friman O . CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2006; 7(10):R100. PMC: 1794559. DOI: 10.1186/gb-2006-7-10-r100. View

4.
Snijder B, Sacher R, Ramo P, Damm E, Liberali P, Pelkmans L . Population context determines cell-to-cell variability in endocytosis and virus infection. Nature. 2009; 461(7263):520-3. DOI: 10.1038/nature08282. View

5.
Lavoie J, LAllemain G, Brunet A, Muller R, Pouyssegur J . Cyclin D1 expression is regulated positively by the p42/p44MAPK and negatively by the p38/HOGMAPK pathway. J Biol Chem. 1996; 271(34):20608-16. DOI: 10.1074/jbc.271.34.20608. View