Comment[ArrayExpressAccession]	E-GEOD-59138
MAGE-TAB Version	1.1						
Public Release Date	2014-07-07
Investigation Title	Deinococcus radiodurans R1 Cells was treated with MMC (5 M-NM-<g/ml) : Control treated with MMC (5 M-NM-<g/ml) vs. bphPR deletion mutant treated with MMC (5 M-NM-<g/ml)						
Comment[Submitted Name]	Deinococcus radiodurans R1 Cells was treated with MMC (5 M-NM-<g/ml) : Control treated with MMC (5 M-NM-<g/ml) vs. bphPR deletion mutant treated with MMC (5 M-NM-<g/ml)
Experiment Description	Transcriptional profiling of Deinococcus radiodurans comparing control wild type cells with bphPR deletion mutant were treated with MMC (5 M-NM-<g/ml) Two-condition experiment, R1 MMC (5 M-NM-<g/ml) vs. bphPR deletion cell MMC (5 M-NM-<g/ml). Biological replicates: 3 control replicates, 3 bphPR deletion mutant 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	Seong Hun	Lim	Im				
Person First Name	Im	Sangyong	Seonghun				
Person Email	lsh1573@nate.com						
Person Affiliation	Korea Atomic Energy Research Institute						
Person Address	Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of KoreaInstitute, Jeongeup, South Korea						
Person Roles	submitter						
Protocol Name	P-GSE59138-1	P-GSE59138-5	P-GSE59138-6	P-GSE59138-2	P-GSE59138-3	P-GSE59138-4	P-GSE59138-7
Protocol Description	The normalization of gene expression by a LOWESS regression was applied for 3 data obtained from 3 biological replicates. The genes were considered to be differentially expressed when the logarithmic gene expression ratios had more than a 2-fold difference in the expression level. The statistical significance of the data was determined by StudentM-bM-^@M-^Ys t test. P-values of less than 0.05 were taken to be statistically significant. ID_REF =  VALUE = Normalized Ratio (average) R1 MMC vs. bphPR MMC	50 M-5g of total RNA were primed with 2 M-5l of 3 M-5g/M-5l random primer at 70M-0C for 10 min, then reversed transcribed at 42M-0C for 2 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 2 M-5l of 50X aminoallyl-dNTP mix, 25 M-5M Cy3-labeling dye and Cy5-labeling dye.	The hybridizations were conducted at 57M-0C for 17 hours in an Agilent Hybridization oven and washed following the manufacturerM-bM-^@M-^Ys protocol (Agilent Technologies, Inc.).	A 10 ml culture grown to the early log phase (OD600 M-bM-^IM-^H 1.0) was treated with MMC (5 M-NM-<g/ml) and incubated for 1 h.	R1 and bphPR deletion mutant cells were cultured O.D 1.0 at the 37 M-0C shaking incubator	Total RNA extracted using RiboEX (GeneAll biotechnology, Korea) following manufacturer's instructions	The scans were performed with an Agilent DNA microarray Scanner (Agilent Technologies, Inc.) using Agilent Feature Extraction software 10.7 (Agilent Technologies, Inc.). The signal intensities were quantified using GeneSpringGX 7.3.1 software (Agilent Technologies, Inc.).
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	GENOTYPE						
Experimental Factor Type	genotype						
Comment[SecondaryAccession]	GSE59138						
Comment[GEOReleaseDate]	2014-07-07						
Comment[ArrayExpressSubmissionDate]	2014-07-07						
Comment[GEOLastUpdateDate]	2014-07-08						
Comment[AEExperimentType]	transcription profiling by array						
Comment[AdditionalFile:Data1]	GSE59138_raw_normalized_data.xlsx						
SDRF File	E-GEOD-59138.sdrf.txt