{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Krzysztof Mikolajczak"],"organism":["Hordeum vulgare"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13358"],"description":["The aim of the study was the elucidation of drought-induced molecular events related to plant hormones occurring in crown tissue of barley, the key organ for cereal survival. Experiments involving large-scale measurements of gene expression at transcript and protein level, hormone abundance, and phenotypic variability in a set of selected barley mutants were carried out to uncover how disturbance of GAs, BRs and SLs homeostasis may affect the barley multivariate response to drought. The characterization included early stages of plant development and continued to the later stages, with observation of effects on the whole-plant architecture and yield formation. The integration of all data allowed to enrich the knowledge of regulatory networks in barley exposed to drought."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA (1-2 µg) was extracted in triplicates using Qiagen RNeasy Plant Mini Kit (Hilden, Germany) according to manufacturer’s instruction. Genomic DNA contamination was removed twice i.e. on-column DNase digestion (RNase-Free DNase Set, Qiagen) and using DNase Max Kit (Qiagen) during and after RNA isolation, respectively.","Library Construction - Library was constructed using library preparation kit: Illumina TruSeq Stranded mRNA (with poly A selection).","Growth Protocol - Drought stress experiment was conducted in the growth chambers under fully controlled conditions. Seeds were sown in pots (H-LSR 4.5 L; 21 cm in diameter and 20 cm in height) filled with a mixture of loamy soil and peat (3:1, w/w) and plants were cultivated in optimal conditions: soil moisture above 70% filed water capacity (FWC), 22°C/16°C day/night, air humidity of 60-70%, a photoperiod of 16/8 h of light/dark.  The number of pots was established so as to contribute with an adequate amount of plant material for all molecular studies along with phenotyping. Biological samples of barley crown tissue for molecular analyses were collected at the beginning of experiment (T0), early stage of drought (3rd day of stress, T1) and at the end of stress application – late drought (10th day of stress, T2). Each replication consisted of crown samples collected from three plants per one pot.","Sample Treatment - Drought (D) was imposed at the tillering stage (23-26 of BBCH code) and maintained for 10 days. Water scarcity was established at 20% FWC and soil moisture in each pot was controlled gravimetrically by weighing and volumetrically (if necessary) using the FOM/mts device. In parallel, the optimal irrigation experiment (C) was carried out.","Sequencing - mRNA sequencing was performed by Macrogen Inc. (Seoul, Republic of Korea) using an Illumina NovaSeq6000 platform with a 150 bp paired-end configuration and the numbers of read pairs from 23.2 to 34.4 M per sample.","Sample Collection - Barley crown tissue was sampled for gene expression analysis using mRNA-seq in three biological replications at two time points: 3 d, tillering stage (23-26 of BBCH code), and 10 d, ten days after the first day. Each replication consisted of crown samples collected from three plants per pot."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Reads of mRNA-seq were mapped in the reference barley genome (IBSC v2, Ensembl Plants rel. 48) using TopHat ver. 2.1.1."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Hordeum vulgare"],"pubmed_authors":["Pawel Krajewski","Anetta Kuczyńska","Krzysztof Mikolajczak"],"additional_accession":[]},"is_claimable":false,"name":"Drought-induced molecular changes in crown of various barley phytohormone mutants","description":"The aim of the study was the elucidation of drought-induced molecular events related to plant hormones occurring in crown tissue of barley, the key organ for cereal survival. Experiments involving large-scale measurements of gene expression at transcript and protein level, hormone abundance, and phenotypic variability in a set of selected barley mutants were carried out to uncover how disturbance of GAs, BRs and SLs homeostasis may affect the barley multivariate response to drought. The characterization included early stages of plant development and continued to the later stages, with observation of effects on the whole-plant architecture and yield formation. The integration of all data allowed to enrich the knowledge of regulatory networks in barley exposed to drought.","dates":{"release":"2023-10-10T00:00:00Z","modification":"2023-09-20T20:12:17.557Z","creation":"2023-09-20T20:12:17.557Z"},"accession":"E-MTAB-13358","cross_references":{"ENA":["ERP151333"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}