Investigation Title	The expression profiles analysis of a virulence plasmid-cured strain of shigella flexneri	
Comment[Submitted Name]	The expression profiles analysis of a virulence plasmid-cured strain of shigella flexneri	
Experimental Design	transcription profiling by array	
Experimental Design Term Source REF	EFO	
Comment[SecondaryAccession]	GSE12535	
Comment[ArrayExpressReleaseDate]	2010-05-15	
Comment[AEMIAMESCORE]	3	
Comment[ArrayExpressAccession]	E-GEOD-12535	
Comment[MAGETAB TimeStamp_Version]	2010-07-30 04:51:05 Last Changed Rev: 13058	
Experimental Factor Name	SHIGELLA FLEXNERI 2A STR. 2457T	
Experimental Factor Type	shigella flexneri 2a str. 2457T	
Experimental Factor Term Source REF	
Person Last Name	Zhu	Wang	
Person First Name	Li	Hengliang	
Person Mid Initials	
Person Email	jewly54@126.com	
Person Phone	
Person Fax	
Person Address	State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie, Fengtai District, Beijing, P.R China	
Person Affiliation	Beijing Institute of Biotechnology	
Person Roles	submitter	
Person Roles Term Source REF	The MGED Ontology	
Quality Control Type	
Quality Control Term Source REF	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2010-05-15	
PubMed ID	
Publication DOI	
Publication Author List	
Publication Title	
Publication Status	
Publication Status Term Source REF	
Experiment Description	In this study, we analyzed the expression profiles of a virulence plasmid-cured strain and wild-type strain of shigella flexneri. The results showed that the genes of glp regulon were upregulated in mutant bacteria in stationary phase cultures. The two strains were cultured in LB broth into log-phase and stationary phase respectively. Then, the total RNAs were extracted and analyzed by Nimblegen biochips.	
Protocol Name	P-GSE12535-14	P-GSE12535-3	P-GSE12535-12	P-GSE12535-13	P-GSE12535-9	P-GSE12535-11	P-GSE12535-2	P-GSE12535-10	P-GSE12535-4	P-GSE12535-5	P-GSE12535-6	P-GSE12535-7	P-GSE12535-8	P-GSE12535-1	
Protocol Type	grow	grow	grow	specified_biomaterial_action	specified_biomaterial_action	specified_biomaterial_action	specified_biomaterial_action	nucleic_acid_extraction	nucleic_acid_extraction	labeling	hybridization	image_aquisition	feature_extraction	bioassay_data_transformation	
Protocol Description	Wild-type bacteria were maintained at TSA plates at 30 degree and cultured in LB broth at 30 degree	Mutant bacteria were maintained at TSA plates at 30 degree and cultured in LB broth at 30 degree	Wild-type bateria were maintained at TSA plates at 30 degree and cultured in LB broth at 30 degree.	Wild-type bacteria were cultured at 30 degree for 9 hours	Mutant bacteria were cultured at 30 degree for 9 hours	wild-type batreria were cultured in LB broth into log-phase (OD=0.6) at 30 degree.	Mutant bacteria were cultured into log-phase (OD=0.6) at 30 degree	use QIAGEN RNAeasy mini kit	use QIAGEN RNAeasy mini kit	Available at manufacturer's website: www.nimblegen.com	Available at manufacturer's website: www.nimblegen.com	Available at manufacturer's website: www.nimblegen.com	Available at manufacturer's website: www.nimblegen.com	ID_REF = <br>VALUE = normalized signal intensity<br>SE_EXPRS = signal confidence<br>PROBE_PAIRS = number of probe pairs	
Protocol Parameters	
Protocol Hardware	
Protocol Software	
Protocol Contact	
Protocol Term Source REF													The MGED Ontology	The MGED Ontology	
SDRF File	E-GEOD-12535.sdrf.txt	
Term Source Name	The MGED Ontology		ArrayExpress	EFO	The MGED Ontology	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php		http://www.ebi.ac.uk/arrayexpress	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version