SRP374450 PRJNA681643 Raw sequence reads from long-term cell culture of Arabidopsis thaliana This work demonstrates the importance of genetic integrity in long term plant cell cultures used as model systems. We show that an established cell culture used in more than 140 independent studies has dysfunctional sugar signalling resulting in an unusual stay-green phenotype at high sugar. With RNA-Seq we show that the transcriptional response to sugar differs significantly from WT, and we link the sugar insensitive phenotype with dysregulation of two transcription factors of a key sugar signalling pathway. Using whole genome sequencing we show that the cell suspension culture has undergone significant genomic variation, and these variations are predicted to impair the function of myriad encoded proteins. The work outlines the importance of monitoring genotype and traits of long-term cell suspension culture stocks. Arabidopsis thaliana