Transcriptome profiling of sorted endoreduplicated nuclei from mature-green tomato fruits

In this study, we have tested the feasibility of a RNA-Seq approach using total nuclear RNA extracted from purified populations of flow cytometry-sorted nuclei based on their DNA content. Nuclei populations from tomato mature-green fruit pericarp tissue were sorted by flow cytometry according to their DNA content. Total nuclear RNA were then extracted. A total of 24 cDNA libraries were then constructed corresponding to 4 ploidy levels (4C, 8C, 16C and 32C) in 3 replicates, with duplex-specific nuclease (DSN) or without (no-DSN) treatment. The multiplex sequencing reaction was performed on an Illumina HiSeq 2000 machine.