{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Magdalena Wójcik-Jagła"],"organism":["Triticum aestivum"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16628"],"description":["The aim of this study was to identify genetic mechanisms of tolerance to active de-acclimation in winter wheat by comparing four tolerant and four susceptible accessions (cultivars and advanced breeding lines). The plants were kept in controlled conditions. 21 days after sowing, the plants were cold acclimated (3 weeks, 4/2 °C, day/night temperature; photoperiod of 10/14 h). Cold acclimation was followed by 7 days of de-acclimating conditions, mimicking a mid-winter warm spell: 12/5°C, day/night temperature; photoperiod of 10/14 h). The fragments of leaves were sampled in three biological replicates (three different plants of the same accession) in three timepoints: just before cold-acclimation (CA-0), after cold-acclimation (CA-21), and after de-acclimation (DA-28). Total RNA samples were sequenced on Illumina NovaSeq 6000 platform in PE150 bp mode. Differences in expression for a given accession were tested between all time-points, averaging the results for three biological replicates. It has been confirmed that active de-acclimation is not simply the inverse of cold acclimation, and that susceptible forms show significantly more changes in expression as a result of de-acclimation than tolerant forms. This provides further support for the hypothesis that tolerance to de-acclimation consists mainly of the absence or weakest response to temperature rise. Among the genes whose expression was significantly altered as a result of de-acclimation, a significant group were genes related to the defence response to stress. In wheat particularly plant hormone related genes, and plant hormones, seem to be playing a crucial role in the response to active de-acclimation, especially ABA and SA. Our results also suggest that in wheat the period of cold-acclimation might be decisive in the later active de-acclimation tolerance."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - The plants were transferred to controlled conditions after sowing (growth chamber, darkness, 25/17 °C), the light (irradiance of 400 μmol m-2s-1 (HPS lamps, SON-T+ AGRO, Philips, Brussels, Belgium), photoperiod of 10/14 h, day/night) was turned on after the plantlets started to emerge. The temperature was lowered to 12°C (day and night) eight days after sowing. 21 days after sowing, the plants were cold acclimated (3 weeks, 4/2 °C, day/night temperature; photoperiod of 10/14 h and irradiance of 250 μmol m-2s-1). Cold acclimation was followed by 7 days of de-acclimating conditions, mimicking a mid-winter warm spell: 12/5°C, day/night temperature; photoperiod of 10/14 h and irradiance of 250 μmol m-2s-1).","Library Construction - Qualified RNA were processed for library construction using the following kits: - NEBNExt PolyA mRNA magnetic isolation module, - NEBNext Ultra II Directional RNA library prep kit - NEBNext UDIs mRNA was isolated by Oligo(dT)-attached magnetic beads. First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with magnetic beads. Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp.","Sequencing - Total RNA samples were sent to weSEQ.IT company for sequencing on Illumina NovaSeq 6000 platform in PE150 bp mode (Illumina, San Diego, CA, USA).","Sample Collection - The 0.05-0.09 g of leaves were sampled in three biological replicates (three different plants of the same accession) in three timepoints: just before cold-acclimation (PH), after cold-acclimation (H), and after de-acclimation (RH), and immediately frozen in liquid nitrogen.","Nucleic Acid Extraction - The 72 frozen leaf samples from 8 accessions, in 3 biological replicates and 3 time-points were subjected to RNA isolation using the combination of Pure Link RNA Mini Kit (Invitrogen, Thermofisher Scientific, Waltham, MA, USA) and spin columns from RNeasy Plant Mini Kit (Qiagen, Hilden, Germany)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The TPM (Transcript Per Million) data transformation was used according to Zhao et al. (2021), J. Transl. Med. 19, 269."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of total RNA"],"species":["Triticum aestivum"],"pubmed_authors":["Magdalena Wójcik-Jagła"],"additional_accession":[]},"is_claimable":false,"name":"Mid-winter de-acclimation triggers stress-like response in cold-acclimated wheat (Triticum aestivum L.)","description":"The aim of this study was to identify genetic mechanisms of tolerance to active de-acclimation in winter wheat by comparing four tolerant and four susceptible accessions (cultivars and advanced breeding lines). The plants were kept in controlled conditions. 21 days after sowing, the plants were cold acclimated (3 weeks, 4/2 °C, day/night temperature; photoperiod of 10/14 h). Cold acclimation was followed by 7 days of de-acclimating conditions, mimicking a mid-winter warm spell: 12/5°C, day/night temperature; photoperiod of 10/14 h). The fragments of leaves were sampled in three biological replicates (three different plants of the same accession) in three timepoints: just before cold-acclimation (CA-0), after cold-acclimation (CA-21), and after de-acclimation (DA-28). Total RNA samples were sequenced on Illumina NovaSeq 6000 platform in PE150 bp mode. Differences in expression for a given accession were tested between all time-points, averaging the results for three biological replicates. It has been confirmed that active de-acclimation is not simply the inverse of cold acclimation, and that susceptible forms show significantly more changes in expression as a result of de-acclimation than tolerant forms. This provides further support for the hypothesis that tolerance to de-acclimation consists mainly of the absence or weakest response to temperature rise. Among the genes whose expression was significantly altered as a result of de-acclimation, a significant group were genes related to the defence response to stress. In wheat particularly plant hormone related genes, and plant hormones, seem to be playing a crucial role in the response to active de-acclimation, especially ABA and SA. Our results also suggest that in wheat the period of cold-acclimation might be decisive in the later active de-acclimation tolerance.","dates":{"release":"2026-03-16T00:00:00Z","modification":"2026-03-16T02:03:20.271Z","creation":"2026-02-10T13:20:26.62Z"},"accession":"E-MTAB-16628","cross_references":{"ENA":["ERP188947"],"Biostudies":["E-MTAB-15311"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0004184"]}}