{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Thijs Zeeuw"],"organism":["Arabidopsis thaliana"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15125"],"description":["Examine the transcriptomic landscape induced by warm temperature and osmotic stress and its dependency on ABA in Arabidopsis detached roots."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - seeds were surface-sterilised and then sowed on 1/10th Murashige and Skoog medium including vitamins (Duchefa Biochemie), supplemented with 0.5 g/ l MES (Duchefa Biochemie) and 0.8% Diashin Agar (Duchefa Biochemie), pH5.8. After 3-4 days of stratification in dark at 4˚C, plates with seed were then placed vertically at 90˚ in a growth chamber for 3 days in white light (100µE, 16h photoperiod, 20˚C) to stimulate germination. At day 3, roots were detached and placed on the same media, supplemented with 5 mM sucrose (Duchefa Biochemie) unless otherwise stated. For osmotic stress and ABA treatments, the medium was additionally supplemented with 25 mM sorbitol (Duchefa Biochemie), 25 mM mannitol (Duchefa Biochemie), 12.5 mM NaCl (Duchefa Biochemie) or 30 nM ABA (Duchefa Biochemie) unless otherwise stated. Root tip position was marked after detachment, and roots were grown in darkness for another 4 days at either 20˚C or 28˚C.","Nucleic Acid Extraction - Samples were ground in Retsch shaker mill with two 1/8” metal ball bearings per sample, at a frequency of 25 Hz for 30 seconds twice. Total RNA was extracted using RNeasy Plant Mini kit (Qiagen), according to manufacturer instructions.","Sample Collection - Detached roots were harvested in dark conditions using a green safe-light and immediately frozen in liquid nitrogen. Each sample comprised material from 40 roots, which were stored at -80 °C until RNA extraction.","Library Construction - RNA poly-A enrichment library preparation were carried out by Novogene.","Sequencing - Sequencing was carried out by Novogene using the illumina NovaSeq 6000 platform","Sample Treatment - seeds were surface-sterilised and then sowed on 1/10th Murashige and Skoog medium including vitamins (Duchefa Biochemie), supplemented with 0.5 g/ l MES (Duchefa Biochemie) and 0.8% Diashin Agar (Duchefa Biochemie), pH5.8. After 3-4 days of stratification in dark at 4˚C, plates with seed were then placed vertically at 90˚ in a growth chamber for 3 days in white light (100µE, 16h photoperiod, 20˚C) to stimulate germination. At day 3, roots were detached and placed on the same media, supplemented with 5 mM sucrose (Duchefa Biochemie) unless otherwise stated. For osmotic stress and ABA treatments, the medium was additionally supplemented with 25 mM sorbitol (Duchefa Biochemie), 25 mM mannitol (Duchefa Biochemie), 12.5 mM NaCl (Duchefa Biochemie) or 30 nM ABA (Duchefa Biochemie) unless otherwise stated. Root tip position was marked after detachment, and roots were grown in darkness for another 4 days at either 20˚C or 28˚C."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Output read quality was assessed in Python using FastQC ​and MultiQC​​, and low quality read trimming was carried out using Trim Galore !​​. The quality of the trimmed reads was assessed again using FastQC and MultiQC, before being mapped to the TAIR10 transcriptome ​using Salmon​."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Arabidopsis thaliana"],"pubmed_title":["Warm temperature and mild water stress cooperatively promote root elongation"],"pubmed_authors":["Thijs Zeeuw","Scott Hayes, Cheuk Ka Leong, Francesca Giaume, Elizabeth van Veen, Wenyan Zhang, Marthe Lamain, Jasper Lamers, Thijs de Zeeuw, Francel Verstappen, Andreas Hiltbrunner & Christa Testerink"],"additional_accession":[]},"is_claimable":false,"name":"RNAseq of temperature and osmotic stress on detached root of Arabidopsis thaliana col-0 and snrk2.2/2.3","description":"Examine the transcriptomic landscape induced by warm temperature and osmotic stress and its dependency on ABA in Arabidopsis detached roots.","dates":{"release":"2025-05-21T00:00:00Z","modification":"2025-05-07T21:10:18.151Z","creation":"2025-05-07T21:10:18.151Z"},"accession":"E-MTAB-15125","cross_references":{"ENA":["ERP172391"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}