MAGE-TAB Version 1.1 Investigation Title 'Microarray analysis of abiotic stress responses in three-week-old Arabidopsis thaliana plants'' rosette leaf tissue for Col-0 wild type plants and double/triple knockout mutants of aquaporins (pip2;1 pip2;2 and pip2;1 pip2;2 pip2;4) treated with drought, heat at different air humidities, or combined drought-heat stress at different air humidities' Experimental Design stimulus or stress design genotype design Experimental Design Term Source REF EFO EFO Experimental Design Term Accession Number EFO_0001762 EFO_0001748 Experimental Factor Name genotype environmental stress block Experimental Factor Type genotype environmental stress block Experimental Factor Term Source REF EFO Experimental Factor Term Accession Number EFO_0000513 Person Last Name Schäffner Georgii Person First Name Anton Elisabeth Person Mid Initials R Person Email schaeffner@helmholtz-muenchen.de elisabeth.georgii@helmholtz-muenchen.de Person Phone Person Fax Person Affiliation Person Address Person Roles investigator submitter Person Roles Term Source REF Person Roles Term Accession Number Quality Control Type Quality Control Term Source REF Quality Control Term Accession Number Replicate Type Replicate Term Source REF Replicate Term Accession Number Normalization Type Normalization Term Source REF Normalization Term Accession Number Date of Experiment 2013-01-31 Public Release Date 2017-06-20 PubMed ID Publication DOI 10.1186/s12870-017-1062-y Publication Author List Elisabeth Georgii, Ming Jin, Jin Zhao, Basem Kanawati, Philippe Schmitt-Kopplin, Andreas Albert, J. Barbro Winkler and Anton R. Schaffner Publication Title Relationships between drought, heat and air humidity responses revealed by transcriptome-metabolome co-analysis Publication Status Publication Status Term Source REF Publication Status Term Accession Number Experiment Description This experiment contains microarray measurements for 135 Arabidopsis thaliana rosette leaf samples covering three genotypes under six different environmental conditions. The three genotypes comprise the Col-0 wildtype and two loss-of-function mutants of aquaporins, a pip2;1 pip2;2 double mutant and a pip2;1 pip2;2 pip2;4 triple mutant (respective AGI locus identifiers: AT3G53420, AT2G37170, AT5G60660). The six conditions include control condition (well-watered, 22°C, 70% relative air humidity), drought stress (one week without watering), heat stress without changing the absolute humidity of the ambient air (6 hours at 33°C, 37% relative air humidity), heat stress with supplemented air humidity to maintain a constant vapor pressure deficit before and during the heat episode (6 hours at 33°C, 84% relative air humidity), and the combinations of drought pretreatment with each of the two heat stress variants (one week of drought followed by 6 hours of heat stress). Samples from all conditions were harvested at the same time (within 15 min starting at 5 p.m.). Protocol Name P-MTAB-50637 P-MTAB-50638 P-MTAB-50635 P-MTAB-50636 P-MTAB-50633 P-MTAB-50634 Protocol Type array scanning and feature extraction protocol normalization data transformation protocol nucleic acid labeling protocol nucleic acid hybridization to array protocol growth protocol nucleic acid extraction protocol Protocol Term Source REF EFO EFO EFO EFO EFO EFO Protocol Term Accession Number EFO_0003814 EFO_0003816 EFO_0003813 EFO_0003815 EFO_0003789 EFO_0002944 Protocol Description Slides were scanned using the Agilent Microarray Scanner, and data were extracted using the Agilent Feature Extraction Software with the template GE1_1010_Sep10. The preprocessing including background correction, quantile normalization and log2 transformation was done with the Bioconductor 2.13 software package limma, version 3.18.13 (Smyth, 2004; Ritchie et al., 2015). Batch effects were corrected using the nlme package in R, version 3.1-115 (Pinheiro et al., 2000). We used cyanine 3-CTP to label the RNA hybridization probes according to the protocol provided by Agilent. 'Transcriptomic analysis was performed using Agilent At8x60K one-color microarrays (Design ID: 29132, A-GEOD-16892) according to the manufacturer''s instructions. The hybridization was done 17h at 65°C, then the slides were washed.' The plants were grown on soil in climate simulation chambers with 11h/13h light/dark cycle (light 08:30 a.m. to 07:30 p.m.), 200 μmol m-2 s-1 photosynthetic photon flux density, 22°C air temperature and 0.79 kPa VPD, corresponding to 70% relative air humidity. Three-week-old plants were flooded with water up to 60% of the pot height for 15 min by an automatic flooding system. After flooding, the plants used for drought stress (D) and combined drought and heat stresses (DH) were stopped being watered and the soil moisture was regularly monitored. When the soil water content dropped to approximately 20% of the initial water content after one week, heat stress (H) was applied to both well-watered plants and drought-treated plants, raising the temperature to 33°C for 6 hours from 11:00 a.m. to 5:00 p.m.. For one set of plants, the absolute air humidity was kept unchanged during the temperature increase, resulting in 37% relative air humidity and 3.17 kPa VPD; this condition is labeled LrH (low relative air humidity). For another set of plants, the heat treatments were done with supplemented air humidity at 84% relative air humidity, to maintain the VPD at 0.79 kPa; the condition is labeled HrH (high relative air humidity). Five replicates of each genotype were generated for each environmental scenario; they were randomly distributed in the chambers to exclude position effects. Each replicate consisted of seven or eight rosettes that were harvested after treatment, collected into plastic bags (4 oz. 118 ml, Whirl-Pak), immediately frozen in liquid nitrogen and stored at -80°C until use. Samples from all conditions were harvested at the same time (within 15 min starting at 5:00 p.m.). Samples were ground at 2500 rpm for 2.5 min using the mixer mill MM 400 (Retsch, Germany), and 100 mg powder were used for RNA extraction. Total RNA was extracted using the RNeasy plant mini kit (Qiagen, Hilden, Germany). RNA quality and quantity was checked with an Agilent Bioanalyzer 2100 (Agilent Technologies, USA) and a Nanodrop ND-1000 spectrophotometer (Kisker-Biotech, Germany). Protocol Parameters Protocol Hardware Protocol Software limma (version 3.18.13), nlme (version 3.1-115) Protocol Contact Term Source Name EFO ArrayExpress Term Source File http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/arrayexpress/ Term Source Version 2.38 SDRF File E-MTAB-4867.sdrf.txt Comment [Submitted Name] 'Microarray analysis of abiotic stress responses in three-week-old Arabidopsis thaliana plants'' rosette leaf tissue for Col-0 wild type plants and double/triple knockout mutants of aquaporins (pip2;1 pip2;2 and pip2;1 pip2;2 pip2;4) treated with drought, heat at different air humidities, or combined drought-heat stress at different air humidities' Comment [AEMIAMEScore] 5 Comment [AEExperimentType] transcription profiling by array Comment[ArrayExpressAccession] E-MTAB-4867 Comment [AEExperimentDisplayName] Microarray analysis of abiotic stress responses in Arabidopsis thaliana rosette leaf tissue of Col-0 wild type plants and double/triple knockout mutants of aquaporins (pip2;1 pip2;2 and pip2;1 pip2;2 pip2;4)