Figure 2 : Monocle orders individual cells by progress through differentiation.

From: The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

Figure 2

(a) An overview of the Monocle algorithm. (b) Cell expression profiles (points) in a two-dimensional independent component space. Lines connecting points represent edges of the MST constructed by Monocle. Solid black line indicates the main diameter path of the MST and provides the backbone of Monocle's pseudotime ordering of the cells. (c) Expression for differentially expressed genes identified by Monocle (rows), with cells (columns) shown in pseudotime order. Interstitial mesenchymal cells are excluded. (d) Bar plot showing the proportion of MEF2C- and MYH2-expressing cells measured by immunofluorescence at the time of collection (top), RNA-Seq at the time of collection (middle) or RNA-Seq at pseudotime (bottom). MEF2C was considered detectably expressed at or above 100 FPKM, MYH2 at 1 FPKM. MEF2C exhibits a bimodal pattern of expression across the cells (not shown), and a threshold of 100 FPKM separates the modes. (e) Expression of key regulators of muscle differentiation, ordered by time collected (cyclin-dependent kinase 1, CDK1; inhibitor of DNA binding 1, ID1; myogenin, MYOG). (f) Regulators from e, ordered by Monocle in pseudotime. Points in e,f are colored by time collected (0 h, red; 24 h, gold; 48 h, light blue; 72 h, dark blue). Error bars, 2 s.d.