Extended Data Fig. 3: Changes in the expression profile of the resting zone upon niche formation.

a, Sections of cartilage at P2 and P28 were imaged before and after cells were captured by LCM for subsequent RNA-seq analysis. b, c, Gene ontology categories enriched by genes significantly upregulated (b) or downregulated (c) in the resting zone at P28 compared to P2. Logarithmic P values of significance are indicated on the x axis. d, Expression heat map for the genes most significantly up- and downregulated between P2 and P28 time points in the resting zone (DESeq2 test with multiple testing correction, FDR < 0.005). e, Heat map of similarities in gene expression between individual samples from the resting and hypertrophic zones from P2 and P28 time points. For each sample, expression of non-redundant PAGODA aspects was calculated and similarity between samples was defined as correlation of aspect expressions (see Methods for details). f–h, Proximal tibial growth plates from P2, P9, P18 and P28 mice were immunostained for CD73 (f), Ki67 (g) or MEF2C (h) and counterstained with DAPI. For a–e, a total of 8 pools of cells from 7 mice were collected at P2 and 7 pools of cells from 7 mice were collected at P28. For f–h, staining was performed in a single experiment (minimum 3 mice) per time point.