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. 2018 Apr 26;7:e31700. doi: 10.7554/eLife.31700

Figure 2. Single cell analysis reveals tissue level differences in robustness of the clock.

(a), Rhythmic cell amplitudes in the imaged sections normalised to the amplitude of the mean trace (green line). Whiskers represent 9th and 91st percentile. (b), Between-cell and within-cell period variability in each imaged section. (c), Stochastic model CCA1 total molecule count for Ω = 1000 (top) and Ω = 100 (bottom) for 100 simulated runs (grey) plotted from 29 to 168 hr in constant light (comparable to the data in Figure 1). Means of all simulated runs are shown in red. Ω represents the system size. (d), Rhythmic simulated run amplitudes for different system sizes (Ω) normalised to the mean simulation (green line). (e), Between and within cell variability of each simulation with different system size. (f), Scatterplot of the rhythmic cells in all imaged plant sections stitched together. Colour indicates the maximum expression. (g), Scatterplot of the maximum expression values vs. longitudinal position on the plant measured from the root tip. Colour legend is the same as (f). For root tip, n = 242; lower root, n = 84; upper root, n = 46; lower hypocotyl, n = 114; upper hypocotyl, n = 53; cotyledon, n = 103 (n = number of rhythmic cells).

Figure 2.

Figure 2—figure supplement 1. Tissue level differences in robustness synchronisation, and period of single cell clock oscillations in repeat WT experiment.

Figure 2—figure supplement 1.

(a), Rhythmic cell amplitudes per section imaged with amplitude of the mean trace overlaid (green line). Whiskers represent 9th and 91st percentile. (b), Between-cell and within-cell period variability in each section. (c), Scatterplot of the rhythmic cells in all imaged plant sections stitched together. Colour indicates the maximum expression value. (d), Scatterplot of the maximum expression values vs. longitudinal position on the plant measured from the root tip. Colour legend is same as (c). (e), Scatterplot of the rhythmic cells in stitched plant sections. Colour indicates the oscillation period. (f), Scatterplot of the period values vs. longitudinal position on the plant measured from the root tip. Colour legend is same as in (e). (g), Sequential montage of the normalised CCA1-YFP expression of rhythmic cells from WT CCA1-YFP repeat. Both colour intensity and spot size indicate expression level. By colour, red indicates low and yellow high intensity. Scale bar represents 0.25 mm. For root tip, n = 200 root (up from tip), n = 46 root (section 1), n = 25 root (sections 2,3,4), n = 70 hypocotyl (section 1), n = 31, hypocotyl (section 2), n = 22; cotyledon, n = 100), n = the number of rhythmic cells.

Figure 2—figure supplement 2. Tissue level differences in robustness, synchronisation, and period of single cell clock oscillations in CCA1-long experiment.

Figure 2—figure supplement 2.

(a), Rhythmic cell amplitudes per section imaged with amplitude of the mean trace per section overlaid (green line). Whiskers represent 9th and 91st percentile. (b), Between-cell and within-cell period variability in each section. (c), Scatterplot of the rhythmic cells in all imaged plant sections stitched together. Colour indicates the maximum expression level per cell. (d), Scatterplot of the maximum expression values vs. longitudinal position on the plant measured from the root tip. Colour legend is same as (c). (e), Scatterplot of the rhythmic cells in all imaged plant sections stitched together. Colour indicates the oscillation period. (f), Scatterplot of the period values vs. longitudinal position on the plant measured from the root tip. Colour legend is same as in (e). (g), Sequential montage of the normalised CCA1-YFP expression of rhythmic cells from CCA1-long line. Both colour intensity and spot size indicate expression level. By colour, red indicates low and yellow high intensity. Scale bar represents 0.25 mm. For root tip, n = 223; root (section 1), n = 111; root (section 2), n = 36; root/hypocotyl, n = 58; hypocotyl (section 1), n = 79; hypocotyl (section 2), n = 88; cotyledon, n = 434), n = the number of rhythmic cells.

Figure 2—figure supplement 3. Periods display no spatial structure in z direction for WT repeat and CCA1-long experiments.

Figure 2—figure supplement 3.

(a–b), Scatterplot in the y-z direction of rhythmic cells for repeat WT experiment in all imaged plant sections (a) or in the root and root tip sections only (b). (c), Scatterplot in the y-z direction of rhythmic cells in the root and root tip sections only for CCA1-long experiment. Whole plant data were not plotted for CCA1-long experiment due to overlap of plant sections in the y-direction. Colour indicates the oscillation period.