Transcriptome analysis using RNA sequencing conducted for wild type (Col-0) and a stable transgenic line with ectopic expression of AT3G11290 (35S:HIN1) under control conditions and after 96 hours at moderate low water potential stress (-0.7 MPa)

RNA sequencing was used to identify alternative splicing events and differentially expressed genes (DEG) in 35S:HIN1 stable transgenic line compared to Col-0 wild type. Two treatments were analyzed for each genotype: unstressed control and a 96 hours moderate severity low water potential (-0.7 MPa) treatment. RNA sequencing analysis found that overexpression of HIN1 in unstressed plants was sufficient to duplicate the effects of stress on nearly 40% of the genes where intron retention was normally suppressed by stress in wild type. Differentially expressed genes (DEGs) were also analyzed (P < 0.05 and fold change ≥ 1.5 used as cut off values for DEGs). Differentially expressed genes in 35S:HIN1has limited overlap of DEGs between 35S:HIN1and wild type. This indicated that HIN1 plays a lesser role in stress-regulated gene expression than in splicing regulation. Wild type (Col-0) and 35S:HIN1 stable transgenic line Arabidopsis thaliana seedlings were germinated on half strength Murashige-Skoog agar plates. After seven days of growth, seedlings were transferred either to fresh plates of control media or to moderate low water potential (-0.7 MPa) imposed using agar plates of the control media infiltrated with PEG-8000. Samples were collected 96 hours after transfer to unstressed control and stress treatments. Three independent biological experiments and RNA extractions were performed for each genotype/treatment. After quality check and quantitation, the samples were used for RNA sequencing. This sequencing experiment was conducted at the same time as analysis of ahl10 describe in Wong et al. (PNAS 2019 116 (6) 2354-2363; https://doi.org/10.1073/pnas.1819971116). Thus the wild type data in this submission are the same as for the ahl10 GEO submission (accesion no. GSE112368).