LincRNAs expressed in specific subpopulations of mESCs and NPCs. LincRNAs expressed in specific subpopulations of mESCs and NPCs. (A) Expression of highly variable lincRNAs (rows; listed in Table S1B) in single cells (columns), clustered by lincRNA expression. Cell types (mESCs in 2i + LIF or serum + LIF, and day 6 and 8 NPCs) and cell cycle stages (assigned by clustering on cell cycle marker gene expression) are indicated at the top. (B) Cell-to-cell variation in expression for mRNAs (grey) and lincRNAs (red), across mESCs (top), or NPCs (bottom), quantified using the DM method (Kolodziejczyk et al, 2015). The median DMs for lincRNAs and mRNAs are listed, and the distributions tested for similarity using the Wilcoxon rank sum test. (C) Scatter plot comparing the 90th expression percentile across single cells versus the median expression, for each lincRNA (red) and mRNA (grey). (D, E) Single cell expression pattern of a highly variable mESC lincRNA (D, Pvt1) and a uniformly expressed mESC lincRNA (E, linc1333), overlaid on the t-SNE projection. (F) An example of correlated lincRNA-mRNA single cell expression across mESC to NPC differentiation, with cells ordered by pseudotime determined using Monocle (Trapnell et al, 2014). (G) Top panels: cell cycle stage assignments for day 8 NPCs based on single cell expression of marker genes (Kolodziejczyk et al, 2015). Bottom panels: examples of three lincRNAs expressed during specific cell cycle stages (XLOC_071380 = G1/S enriched, and Miat and Rmst = G2/M enriched). For each lincRNA, the heat bars show expression levels across the 67 G1/S cells (top bar) and 48 G2/M cells (bottom bar). In (B, C), key lincRNAs selected for detailed exploration are highlighted in green. See also Fig S1 and Tables S1A, B, and S3. Alex C Tuck et al. LSA 2018;1:e201800124 © 2018 Tuck et al.