{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Hans van Veen"],"organism":["Arabidopsis thaliana"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15812"],"description":["RNA sequencing (RNA-seq) was performed to investigate potential roles of the unfolded protein response in submergence and recovery responses of Arabidopsis thaliana. Plants were grown to the 10-leaf stage and then subjected to 4 days of complete submergence. Samples were collected at four time points: prior to submergence (T0), after 1 day of submergence (1d), after 4 days of submergence (4d - end of submergence period), and 3 hours after de-submergence (recovery). For each time point, rosettes were collected and divided into two developmental zones: (i) old leaves (leaves 1 to 5) and (ii) young leaves (leaves 6 to 10 including the shoot apical meristem (SAM)). There were three biological replicates per tissue type of each genotype at each time point. Each biological replicate consisted of tissue pooled from two plants. Two genotypes were examined: Col-0 (wild type) and the bzip60/bzip28 double mutant, which is impaired in unfolded protein response signaling. RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA protocol and sequenced on an Illumina platform to generate paired-end reads."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - TruSeq stranded mRNA","Growth Protocol - Pots with seeds were germinated and grown in a growth chamber (20°C, 200 μmol m‐2 s‐1 photosynthetically active radiation (PAR), a 9-hour photoperiod from 8:00 to 17:00, and 70% relative humidity). Pots were thinned when seedlings were at 2-leaf stage (with 2 true leaves and 2 cotyledons), so there was only one seedling per pot. Plants were grown to the 10-leaf stage before they were used for experiments.","Sample Collection - leaf blades of leaf 3 (old leaf) and leaf 7 (young leaf) were harvested before submergence, after 2 and 4 days of submergence, and after 1, 3, 6, and 24 hours of recovery (Figure 1). 8-16 leaf blades were pooled together per biological replicate. For the Col-0 and bzip28/60 RNA-seq, Arabidopsis plants were harvested before submergence, after 1 and 4 days of submergence, and after 3 hours of recovery in the light. Old (leaves 1-5) and young (leaves 6-10 and the meristem) halves of the rosettes were harvested separately.","Nucleic Acid Extraction - RNAseq experiments, RNA was isolated using the RNeasy Plant Mini Kit (Qiagen), residual genomic DNA was digested using on-column DNase-I digestion (Ambion).","Sample Treatment - Flooding treatments were as described previously (Rankenberg et al. 2024, https://doi.org/10.1016/j.xplc.2024.100848)","Sequencing - Illumina NovaSeq 6000"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - HISAT2 and htseq","Data Transformation - TMM normalization with EdgeR and Limma"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Arabidopsis thaliana"],"pubmed_authors":["Maria Angelica Sanclemente","Rashmi Sasidharan","Hans van Veen"],"additional_accession":[]},"is_claimable":false,"name":"Leaf age determines flood resilience through distinct submergence and recovery effects","description":"RNA sequencing (RNA-seq) was performed to investigate potential roles of the unfolded protein response in submergence and recovery responses of Arabidopsis thaliana. Plants were grown to the 10-leaf stage and then subjected to 4 days of complete submergence. Samples were collected at four time points: prior to submergence (T0), after 1 day of submergence (1d), after 4 days of submergence (4d - end of submergence period), and 3 hours after de-submergence (recovery). For each time point, rosettes were collected and divided into two developmental zones: (i) old leaves (leaves 1 to 5) and (ii) young leaves (leaves 6 to 10 including the shoot apical meristem (SAM)). There were three biological replicates per tissue type of each genotype at each time point. Each biological replicate consisted of tissue pooled from two plants. Two genotypes were examined: Col-0 (wild type) and the bzip60/bzip28 double mutant, which is impaired in unfolded protein response signaling. RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA protocol and sequenced on an Illumina platform to generate paired-end reads.","dates":{"release":"2025-11-15T00:00:00Z","modification":"2026-05-27T17:40:23.485Z","creation":"2025-10-21T16:27:10.08Z"},"accession":"E-MTAB-15812","cross_references":{"ENA":["ERP182601"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}