Comment[ArrayExpressAccession] E-GEOD-52545 MAGE-TAB Version 1.1 Public Release Date 2013-11-21 Investigation Title Transcriptomics of cryophilic Saccharomyces kudriavzevii reveals the key role of gene translation efficiency in cold stress adaptations Comment[Submitted Name] Transcriptomics of cryophilic Saccharomyces kudriavzevii reveals the key role of gene translation efficiency in cold stress adaptations Experiment Description Comparative genome-wide gene expression analysis between a wine yeast strain belonging to the species S. cerevisiae and the type strain from S. kudriavzevii IFO1802, a cryotolerant yeast, in natural must fermentations. RNA samples taken from wine fermentations at 12M-BM-:C and 28M-BM-:C at the beginning of exponential phase. Three biological replicates. 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 Tronchoni Tronchoni Medina GuillamM-CM-3n Querol PM-CM-)rez-Torrado Person First Name Jordi Jordi Victor Jose Amparo Roberto Person Mid Initials M Person Email tronchoni@gmail.com Person Affiliation CSIC Person Address CSIC, Avda. AgustM-CM--n Escardino, 7, Paterna, Spain Person Roles submitter Protocol Name P-GSE52545-1 P-GSE52545-4 P-GSE52545-5 P-GSE52545-2 P-GSE52545-3 P-GSE52545-6 Protocol Description Raw data with a global background subtraction were generated from GenePix pro 6.0. Analyses were done using Acuity 4.0 software (Molecular Devices, CA, USA).The individual data sets were normalized to a log2 ratio value of 1. After normalization, data were filtered to remove spots flagged as not found. Genes with a two-fold log2 ratio values were considered to be significantly expressed. ID_REF = VALUE = log2 ratio (635/532) 2-4 ug of total RNA was linearly amplified using the Low RNA Input Fluorescent Linear Amplification kit (Agilent TechnologiesM-bM-^DM-", Ca, USA). 2-3 ug of amplified cRNA was used as template for cDNA synthesis. cDNA was marked indirectly with M-bM-^@M-^\SuperScriptM-bM-^DM-" Indirect cDNA Labeling SystemM-bM-^@M-^] (InvitrogenM-bM-^DM-", SanDiego, CA). A mixture of 200 to 300 pmol of the two samples labelled was concentrated in a Concentrator Plus (EppendorfM-bM-^DM-", Hamburg, Germany). Competitive hybridization was performed in hybridization chambers AHC (ArrayIt Corporation, CA, USA) at 42M-0C overnight. (Prehybridization solution contained 3X SSC, 0.1% SDS and 0.1 mg/ml BSA; hybridization solution Wine fermentations in Tempranillo must at 12M-:C or 28M-:C RNA extraction method was based on consecutive treatments with phenol-tris, phenol-chloroform (5:1) and chloroform-isoamyl alcohol (24:1) and a final precipitation with ethanol and sodium acetate (Garcia-Martinez et al., 2004). Signal intensities of Cy3 and Cy5 were acquired with an Axon GenePix 4100A scanner (Molecular devices, CA, USA) using GenePix Pro v.6.1 software, at a resolution of 10 M-NM-