Comment[ArrayExpressAccession] E-GEOD-42060 MAGE-TAB Version 1.1 Public Release Date 2012-11-07 Investigation Title Partial deficiency of isoleucine impairs alters transcript levels of the genes involved in branched-chain amino acid and glucosinolate metabolism in Arabidopsis Comment[Submitted Name] Partial deficiency of isoleucine impairs alters transcript levels of the genes involved in branched-chain amino acid and glucosinolate metabolism in Arabidopsis Experiment Description Isoleucine (Ile) is one of the branched-chain amino acids (BCAAs) that are essential substrates for protein synthesis in all organisms. In this study, we characterized an Arabidopsis mutant, lib (low isoleucine biosynthesis), that has defects in both cell proliferation and cell expansion processes during root development. This mutant carries a mutation in OMR1 gene that encodes a threonine deaminase/dehydratase (TD) which results in a defect in isoleucine production. Microarray analysis indicated that the partial deficiency of Ile in the lib mutant triggers a decrease in transcript levels of the genes encoding the major enzymes involved in the BCAA degradation pathway; the analysis also indicated that many genes involved in the biosynthesis of methionine-derived glucosinolates are up-regulated. Total RNAs were isolated from three replicate samples of the root tissues of 8-day-old wild type (w) and lib mutant (m)seedlings grown on 1/2 MS medium and hybridized on Affymetrix ATH1 microarrays. The changes of gene expression in the lib mutant (m) was compared with the wild type (w). The corrected P value of <0.05 was used to select the genes for comparison, and only those genes whose expression was two-fold higher or lower in lib than in the WT were used for analysis. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Liu Liu Yu Person First Name Dong Dong Hailan Person Email liu-d@mail.tsinghua.edu.cn Person Affiliation Tsinghua University Person Address Tsinghua University, School of Life Sciences, Beijing, China Person Roles submitter Protocol Name P-GSE42060-1 P-GSE42060-6 P-GSE42060-3 P-GSE42060-8 P-GSE42060-7 P-GSE42060-2 P-GSE42060-4 P-GSE42060-5 Protocol Description ID_REF = VALUE = MAS5.0 signal intensity ABS_CALL = Array hybridization and wash were performed using GeneChipM-. Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA US) following the manufacturerM-bM-^@M-^Ys instructions. The sterilized Arabidopsis seeds were sown on Petri dishes containing a medium of 1/2 Murashige & Skoog (MS) basal salts with 1% sucrose, 0.1% MES (adjusted to pH 5.7 with 1 N NaOH), and 1.2% agar. After 2 days of stratification at 4M-bM-^DM-^C, the agar plates were placed vertically in the growth room with a photoperiod of 16 h light : 8 h dark at 22M-bM-^@M-^S24M-bM-^DM-^C.The light intensity was 100 M-5mol m-2 s-1. At day 8 after seed germination, whole seedlings were collected for RNA isolation. Raw data were normalized by the MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). Microarray data analysis was performed using the SBC Analysis system, which is available on the website: http://sas.ebioservice.com/index.jsp. The username and password to access to this website are available upon request. Hybridized slides were scanned by GeneChipM-)Scanner 3000 (Cat00-00212, Affimetrix, Santa Clara, CA US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA US) with default settings. No treatment is applied. Trizol extraction of total RNA was performed using RNA extraction kit (Cat#15596-018M-oM-