Fig. 3. Light induces an increase in transcriptome size in cotyledon cells during de-etiolation.

A The analyses employed cotyledons dissected from 5-day-old seedlings grown in darkness (Dark) and exposed to light for the indicated duration (0, 1, 6, and 24 h). Five independent biological replicates were analyzed for each time point. B Transcriptome size of the five biological replicates was estimated from the size factor of DESeq2 differential analyses of Standard RNA-seq and Spike-in RNA-Rx, divided by library size. For comparison, the median values of the Dark samples were arbitrarily set to 1. One dot represents the value for one biological replicate at each time point. C Distribution of mean transcript levels and Log₂ FC of expression. The Dark time point was used as a reference for each Standard RNA-seq and Spike-in RNA-Rx analysis. Source data are provided as a Source Data file. D Number of differentially expressed genes (DEGs, q-value < 0.01 for a |Log2 FC | > 0.5) in standard RNA-seq and Spike-in RNA-Rx analyses. The Venn diagrams show the number of DEGs commonly called by both methods (see Supplementary Data 3). E Log₂ FC of expression at the three time points of light exposure compared to the Dark time point for all genes analyzed in D. Genes are ranked according to their Log₂ FC at the 24 h time point. F Heatmap representing the Log₂ FC of expression at the indicated time points compared to the Dark time point for genes ordinarily used as RT-qPCR references or considered as housekeeping. Genes are ranked by their Log₂ FC at the 24 h time point. The sidebar indicates which gene sets were called DEGs in Standard RNA-seq or Spike-in RNA-Rx analyses, using the color code shown in D.