Comment[ArrayExpressAccession] E-GEOD-49528 MAGE-TAB Version 1.1 Public Release Date 2013-08-03 Investigation Title Comparative transcriptional analysis of Desulfovibrio alaskensis G20, a choline utilization regulator and LysX Comment[Submitted Name] Comparative transcriptional analysis of Desulfovibrio alaskensis G20, a choline utilization regulator and LysX Experiment Description Expression data for Desulfovibrio alaskensis strain G20 and mutants in regulator proteins grown on lactate sulfate media and then pelleted and transferred to another media when they reached stationary phase. The Choline mutant was transferred to lacte/sulfate minimal media and choline/sulfate minimal media. The LysX mutant was transferred to minimal media with lysine and rich media. G20 was transferred to minimal media, choline/sulfate minimal media, lactate/choline/sulfate minimal media, minimal media with lysine, and rich media. We aimed to confirm or expand the regulons of each of the transposon interupted regulator mutants and compare gene expression responses of the regulators in different growth conditions. 10 samples were collected: 2 regulator mutants (2 conditions each), Desulfovibrio alaskensis G20 (5 conditions), 2 replicates for G20 minimal media condition. Control sample -G20 rich media. 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 Kuehl Kuehl Price Deutschbauer Arkin Novichkov Rodionov Person First Name Jennifer Jennifer Morgan Adam Adam Pavel Dmitry Person Mid Initials V V M P Person Email jvkuehl@lbl.gov Person Affiliation Lawrence Berkeley National Laboratory Person Phone 5106435683 Person Address Physical Biosciences, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California, USA Person Roles submitter Protocol Name P-GSE49528-1 P-GSE49528-5 P-GSE49528-6 P-GSE49528-2 P-GSE49528-3 P-GSE49528-4 P-GSE49528-7 Protocol Description Quantile normalized the probe intensities to match the G20 rich lactate/sulfate media, averaged the log2 values for each gene and set the median log2 expression level in each sample to zero. ID_REF = VALUE = Log2 expression level of each gene Prepared first-strand labeled cDNA with SuperScript Plus Indirect cDNA Labeling Module (Invitrogen). Standard NimbleGen protocol. We transferred pellets to new media, resuspended the pellets, waited one hour, then collected the pellets and stored them in -80C until RNA extraction. The choline mutant was transferred to a 30 mM choline/ 30 mM sulfate media and a lactate/sulfate media. The lysX mutant was transferred to minimal media with .3 mM lysine and to rich media (.1% Yeast extract). G20 was transferred to choline/sulfate media, a lactate/sulfate media, a lactate/choline/sulfate media, a rich lactate/sulfate media, a minimal lactate/sulfate media with lysine. We collected expression data of Desulfovibrio alaskensis str. G20 and 2 mutants with transposon insertions in regulator proteins. We grew the cultures in minimal 60 mM lactate/ 30mM sulfate media in an anaerobic chamber at 30C until cells reached early stationary phase. Basal salts - 8mM MgCl2, 20mM NH4Cl, 2mM K2PO4 (dibasic), .6mM CaCl2, 30mM Tris-HCl. Thauer's vitamins and trace elements. Isolated total RNA with RNeasy mini kit (Qiagen). Standard NimbleGen protocol. Protocol Type normalization data transformation protocol labelling protocol hybridization protocol sample treatment protocol growth protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name CARBON SOURCE ADDED NUTRIENT GENOTYPE Experimental Factor Type carbon source added nutrient genotype Comment[SecondaryAccession] GSE49528 Comment[GEOReleaseDate] 2013-08-03 Comment[ArrayExpressSubmissionDate] 2013-08-02 Comment[GEOLastUpdateDate] 2013-08-05 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-49528.sdrf.txt