Fig. 5. Genes with stable absolute expression recapitulate spike-in information in independent studies of cotyledon de-etiolation.

A The pipeline used to identify reference genes with stable absolute expression levels during cotyledon de-etiolation led to the selection of 32 genes (see “Methods” for details). TPM values from the five biological replicates at the four time points (Dark, 1 h, 6 h and 24 h) were used. Created in BioRender. Richet-Bourbousse, C. (2025) https://BioRender.com/rj05ueh. B Identity of the selected stable genes. C MA-plot analyses after Standard RNA-seq or Spike-in RNA-Rx, highlighting the 32 stable genes (orange). D Differential gene expression in our study and in 3 published datasets^8,9,13 using the set of 32 stable genes as an internal reference for normalization. In each analysis, the dark time point was used as a reference. E Number of differentially expressed genes (q-value < 0.01 for a |Log2 FC | > 0.5) using the 32 reference genes as an internal control for normalization of our RNA-seq data and of the same published datasets as in (D).