Extended Data Fig. 9: Effect of GATC motif on expression across root cell types.

(a) GATC-effect sizes across root cell types, as quantified in Fig. 5g. Gene expression was averaged from scRNA-seq data based on published cell annotations³³. QC - Quiescent center; LRC - Lateral root cap; CC - companion cell; PPP - phloem pole pericycle; XPP - xylem pole pericycle. (b) GATC-effect sizes visualized for different root cell types (x-axis) across root developmental stages (y-axis). Analysis uses cases with at least 150 cells intersecting the two definitions. Gray rectangles indicate cases below this threshold. The quiescent center, defined only as meristematic, is excluded. (c) Given that each single cell only provides data on a subset of genes, we used an alternative method to quantify the GATC-motif effect at the single-cell level. For each cell, mRNA counts from genes with a GATC motif were divided by the total mRNA count. This approach is more robust for sparse data. The quantities plotted reveal significant changes in mRNA species across root developmental stages. Boxplots show the median (center line), IQR (box bounds), whiskers (min and max within 1.5 IQR), and outliers (points beyond whiskers). Number of cells per category is indicated. (d) The mRNA percentage from GATC-motif-containing genes is depicted for each of the 110,000 cells in the single-cell Arabidopsis root atlas map³³ (e) Root developmental stage definitions from ref. ³³, presented as in their original study for comparison.