Nuclei were isolated using a modified INTACT protocol. RNA was extracted from nuclei using proteinase K treatment, followed by Trizol extraction and RNeasy micro columns. RNA quality was assessed using Bioanalyzer and Qubit. Libraries were prepared using TruSeq Stranded Total Plant RNA with Ribo-Zero Plant, employing rRNA depletion. Sequencing was performed on NextSeq500, generating 30 million 75bp reads per sample. Samples were sequenced in triplicate, except KAT1:INTACT at 40% SWC (duplicate) and 20% SWC (quadruplicate).