Fig. 3

a Principal component analysis (PCA) of global gene expression from different biological replicates of RNA samples for RNA-seq. Expression estimates were log-transformed and subjected to PCA using a covariance matrix. The biological replicates clustered together, whereas the different cell types were distinct. b A pie chart representing the number of differentially expressed genes from DRNL::GFP ap1 cal apices. Out of 24,918 expressed transcripts (NRC ≥ 1 in the GFP+/GFP− comparison in at least one of the type of protoplasts), the proportion significantly up-regulated (p ≤ 0.01; fold-change ≥ 1.5 light and dark-red; fold-change ≥ 2.0 dark red) or downregulated (p ≤ 0.01; fold-change ≥ 1.5 light and dark-green; fold-change ≥ 2.0 dark green) in GFP+ protoplasts compared to GFP– protoplasts is shown. c The log₂ (relative transcript expression) for DÖRNRÖSCHEN-LIKE (DRNL), ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 (AHP6), HEAT-SHOCK PROTEIN70 (HSP70) and BREVIPEDICELLUS (BP) is depicted as a ratio from GFP+/GFP− protoplasts determined by qPCR or taken from the RNA-seq data. Additionally, differences in the expression of the four genes in unsorted protoplasts vs. whole apices of ap1 cal inflorescences were analysed via qPCR