Extended Data Fig. 5: Identification of cell cycle associated lncRNAs.

(A) Scatter plot highlighting the 50 most variable cell cycle genes on top of a scatter plot showing mean and standardized variance in expression over cells. (B) Low dimensional PCA projections of cells based on the most variable genes identified in (A). Cells are colored according to the annotated cell cycle phase. (C) Expression pattern of representative marker genes across cells, ordered according to cell cycle progression. The expression represents a sliding window (width = 15) of the mean expression. Colors represent marker genes for the individual cell cycle phases. (D) Scatter plot representing the mean expression of cell cycle genes in mouse primary fibroblasts (n = 533 cells) against lentiviral transduced (shRNA-Control) NIH/3T3 (n = 147 cells). R represents the Spearman correlation. (E) Cell cycle distribution of NIH/3T3 cells upon various cell cycle synchronizations by indicated compounds. (F) Relative expression measured by RT-qPCR of two cell cycle marker genes upon cell cycle synchronization in NIH/3T3 cells. Samples were standardized to DNase treated RNA input. (G) Relative expression measured by RT-qPCR for candidate lncRNAs upon cell cycle synchronization in NIH/3T3 cells. Samples were standardized to DNast treated RNA input. (E-G; n = 4 biologically independent samples, data presented as mean values + /- s.e.m., p-values represent a two-sided Student’s t-test).