Protocol to study mRNA levels during endoreplication in Arabidopsis thaliana through nuclei extraction and a sorting strategy.

In plants, differentiation and expansion of some cell types is accompanied by exit from cell division and onset of endoreplication. Here, we describe a protocol to study changes in mRNA levels during endoreplication in Arabidopsis thaliana cotyledons. We provide detailed steps for the isolation of total nuclei and a strategy to sort stained nuclei according to their ploidy level. Finally, we detail procedures for RNA extraction, a housekeeping gene, and a marker gene for qPCR across ploidy.