Comment[ArrayExpressAccession] E-GEOD-56387 MAGE-TAB Version 1.1 Public Release Date 2014-04-01 Investigation Title Expression analysis of Vibrio cholerae O395N1 delta-nqrA-F mutant Comment[Submitted Name] Expression analysis of Vibrio cholerae O395N1 delta-nqrA-F mutant Experiment Description Investigation of whole genome gene expression level changes in a Vibrio cholerae O395N1 delta-nqrA-F mutant, compared to the wild-type strain. Total RNA recovered from wild-type cultures of VIbrio cholerae O395N1 and its nqrA-F mutant strain. Each chip measures the expression level of 3,835 genes from Vibrio cholerae O1 biovar eltor str. N16961 with twenty average probes/gene, with five-fold technical redundancy. 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 Hase Rosato Minato Person First Name Claudia Caprice Yusuke Person Email geo@ncbi.nlm.nih.gov Person Affiliation Oregon State University Person Address Oregon State University, 105 Magruder Hall, Corvallis, USA Person Roles submitter Protocol Name P-GSE56387-1 P-GSE56387-4 P-GSE56387-5 P-GSE56387-2 P-GSE56387-3 P-GSE56387-6 Protocol Description The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package. ID_REF = VALUE = RMA Labeling was performed by NimbleGen standard operating protocol. See www.nimblegen.com. Hybridization was performed by NimbleGen standard operating protocol. See www.nimblegen.com. Vibrio cholerae O395N1 was grown to early-log phase (O.D.600nm 0.2) aerobically at 30M-0C in LB (pH6.5). Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by TURBO DNA-freeM-bM-^DM-" Kit (Ambion). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Center for Genome Research and Biocomputing (Oregon State University, Corvallis, OR USA). Scanning was performed by NimbleGen standard operating protocol. See www.nimblegen.com. Protocol Type normalization data transformation protocol labelling protocol hybridization protocol growth protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name GENOTYPE Experimental Factor Type genotype Comment[SecondaryAccession] GSE56387 Comment[GEOReleaseDate] 2014-04-01 Comment[ArrayExpressSubmissionDate] 2014-03-31 Comment[GEOLastUpdateDate] 2014-04-01 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-56387.sdrf.txt