Extended Data Fig. 5: Analysis of circadian gene expression in SCN neuron subtypes.
From: Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus
a, Circadian rhythmicity of 5 SCN neuron subtypes and 10 non-SCN neuron subtypes. Rhythmicity of core clock genes (left). Percentage of rhythmic genes in total expressed genes in each neuron subtype (right). N14 and N15 subtypes were excluded in this analysis due to their small number of cells. P-values were calculated with JTKCycle. b, smFISH showing the expression patterns of Grp (green) and Bmal1 (red) in SCN at ZT14. DAPI signals in blue indicate cell body positions. Scale bar is 100 μm. c, Quantification and comparison of Bmal1 expression among Grp+ cells within SCN (n=87), Grp- cells within SCN (n=711) and non-SCN cells (n=1521). The boxplots indicate the minimum, maximum, first quartile, third quartile and outliers of the distribution of single-cell Bmal1 expression. p-values are calculated by ANOVA with Dunnett correction. d, smFISH showing the expression of Per2 (red), Vip (green) and Cck (white) in SCN at 6 circadian time points. Scale bar represents 10μm. e, Quantification of circadian expression of Per2 in Vip+ and Cck+ neurons by the number of Per2 counts in each type of neurons in SCN. The boxplots indicate the median, minimum, maximum, first quartile and third quartile of the distribution of single-cell Per2 expression. Circadian phase (φ) and its error were analyzed by cosine regression on the population median values of each subtype at each time point. The numbers of Vip+ neurons used in the analysis: n=178 (CT14); n=197 (CT18); n=240 (CT22); n=195 (CT26); n=229 (CT30); n=206 (CT34). The numbers of Cck+ neurons used in the analysis: n=226 (CT14); n=250 (CT18); n=305 (CT22); n=248 (CT26); n=291 (CT30); n=262 (CT34). P-values of comparisons between peak and trough values using two-sided Mann-Whitney U-test are p=1.3x10-38 (Vip+) and p=7.3x10-10 (Cck+). P-values are represented as * p<0.05, ** p<0.01, *** p<0.001.
