We present and propose the application of 5-Ethynyl uridine for metabolic labeling of RNAs in plants, which allows the isolation of neo-synthesized RNAs from intact plants. This system provides the possibility to investigate neo-synthesized RNAs from living plant cells. Neu-RNAseq can be applied for the detection of splicing variants, especially RNAs containing retained introns and alternative 5' and 3' splice sites. A subset of unspliced RNAs identified by Neu-Seq is subjected for elimination by the NMD pathway, but the majority of the RNA splicing variants detected in Neu-Seq libraries will be further processed into mature mRNAs. Overall design: RNA synthesized within 1 hour was analyzed in comparison to a steady-state transcriptome from the same source material. Samples were analysed in triplicates.