Investigation Title Expression data from Arabipdosis msh1 recA3 double mutant under heat stress Comment[Submitted Name] Expression data from Arabipdosis msh1 recA3 double mutant under heat stress Experimental Design genetic modification design Experimental Design Term Source REF EFO Comment[AEExperimentType] transcription profiling by array Comment[AEExperimentDisplayName] Transcription profiling by array of Arabidopsis msh1 recA3 double mutants under heat stress Comment[AEMIAMESCORE] 4 Comment[SecondaryAccession] GSE19603 Comment[ArrayExpressReleaseDate] 2010-04-12 Comment[Publication DOI] 10.1104/pp.109.152827 Comment[ArrayExpressAccession] E-GEOD-19603 Comment[MAGETAB TimeStamp_Version] 2010-08-04 01:52:12 Last Changed Rev: 13058 Experimental Factor Name genotype environmental stress Experimental Factor Type genotype environmental stress Experimental Factor Term Source REF Person Last Name Davila Shedge Person First Name Jaime Vikas Person Mid Initials Person Email jdavila2@unl.edu Person Phone Person Fax Person Address Plant Science Innovation Center, University of Nebraska, 1901 Vine Street, Lincoln, NE, USA Person Affiliation University of Nebraska Person Roles submitter Person Roles Term Source REF Quality Control Type Quality Control Term Source REF Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2010-04-12 PubMed ID 20139171 Publication DOI 10.1104/pp.109.152827 Publication Author List Shedge V, Davila J, Arrieta-Montiel MP, Mohammed S, Mackenzie SA Publication Title Extensive rearrangement of the Arabidopsis mitochondrial genome elicits cellular conditions for thermotolerance. Publication Status published Publication Status Term Source REF EFO Experiment Description In Arabidposis thaliana, the msh1 recA3 double mutant shows an extensive mitochondrial genome rearrangement and displays pronounced thermotolerance. We use microarray analysis to characterize genes and their response in the double mutant to a heat shock experiment in which plants were exposed to a temperature of 37 C for 2 hours. Wild type and double mutant plant were exposed to a temperature of 37 C for 2 hours and RNA samples were collected for the wild type and the double mutant before and after the heat shock. Protocol Name P-GSE19603-2 P-GSE19603-3 P-GSE19603-4 P-GSE19603-5 P-GSE19603-6 P-GSE19603-7 P-GSE19603-8 P-GSE19603-1 Protocol Type specified_biomaterial_action grow nucleic_acid_extraction labeling hybridization image_aquisition feature_extraction bioassay_data_transformation Protocol Description For heat treatment experiments, 8-week-old plants were first transferred to a chamber (Percival Scientific) where they were subjected to heat stress at 37C for approximately 24 hours. Cold treated seeds were sown directly on soil (Metro Mix 360) and kept in growth chambers at 8- hour daylength at 24 C for 8 weeks and then transferred to a growth chamber with 16-hour daylength at 24 C. total RNA was extracted from above-ground parts of 8-week-old Col-0 plants and msh1 recA3 double mutant plants (Col-0 background) using TRIzol (Invitrogen) extraction procedure followed by purification on Rneasy columns (Qiagen). According to Affymetrix instructions RNA was hybridized to individual Affymetrix GeneChip oligonucleotide ATH1 array using manufacturers instructions According to Affymetrix instructions Expression data from Affymetrix genechips were normalized using the Robust Multichip Average (RMA) method using Bioconductor’s affy package in the R language ID_REF =
VALUE = RMA signal intensity Protocol Parameters Protocol Hardware Protocol Software Protocol Contact Protocol Term Source REF SDRF File E-GEOD-19603.sdrf.txt Term Source Name EFO Term Source File http://www.ebi.ac.uk/efo/ Term Source Version