Investigation Title	Transcription profiling of RNA from mouse liver or spleen was vs a sample from cultures or to genomic DNA
Comment[Submitted Name]	Bm_invivo-exp1
Experimental Design	growth_condition_design	pathogenicity_design	transcription profiling by array
Experimental Design Term Source REF	mo	mo	EFO
Comment[ArrayExpressReleaseDate]	2005-05-15
Comment[AEMIAMESCORE]	5
Comment[ArrayExpressAccession]	E-MEXP-334
Comment[MAGETAB TimeStamp_Version]	2011-07-29 18:30:12 Last Changed Rev: 14857
Experimental Factor Name	Nutrients (live mouse)	Extracted material	Atmosphere	Nutrients
Experimental Factor Type	nutrients	material_type	atmosphere	nutrients
Experimental Factor Term Source REF
Person Last Name	Kim
Person First Name	H. Stanley
Person Mid Initials
Person Email	hstanleykim@korea.ac.kr
Person Phone	301-795-7846
Person Fax
Person Address	9712 Medical Center Dr., Rockville, MD, 20850, USA
Person Affiliation	Microbial Genomics, TIGR
Person Roles	submitter
Person Roles Term Source REF	mo
Quality Control Type	dye_swap_quality_control
Quality Control Term Source REF	The MGED Ontology
Replicate Type
Replicate Term Source REF
Normalization Type
Normalization Term Source REF
Date of Experiment
Public Release Date	2005-05-15
PubMed ID	16336651
Publication DOI	10.1186/1471-2164-6-174
Publication Author List	Kim HS, Schell MA, Yu Y, Ulrich RL, Sarria SH, Nierman WC, DeShazer D.
Publication Title	Bacterial genome adaptation to niches: divergence of the potential virulence genes in three Burkholderia species of different survival strategies.
Publication Status
Publication Status Term Source REF
Experiment Description	In each experiment, RNA from mouse liver or spleen was compared to a sample from cultures or to genomic DNA.
Protocol Name	P-MEXP-8576	P-MEXP-8575	P-MEXP-8577	P-MEXP-8579	P-MEXP-8578	P-MEXP-8580	P-MEXP-8583	P-MEXP-8581	P-MEXP-8582	P-MEXP-8584	P-MEXP-8587
Protocol Type	specified_biomaterial_action	grow	pool	nucleic_acid_extraction	nucleic_acid_extraction	labeling	labeling	labeling	labeling	hybridization	bioassay_data_transformation
Protocol Description	Female BALB/c mice were obtained from Charles River Laboratories (National Cancer Institute, Frederick, MD) and were 6- to 8-weeks-old at the time of use. Three mice were injected intraperitoneally with 1.5 x 10<sup>7</sup> B. mallei ATCC 23344 (21 times the 50% lethal dose) and provided with rodent feed and water ad libitum and maintained on a 12-h light cycle. Two days postinfection the mice were euthanized in a CO2 chamber and spleens and livers were removed and homogenized in 1 ml of Trizol (Invitrogen Corp., Carlsbad, CA). RNA was purified following the recommended protocol from the manufacturer. Research was conducted in compliance with the Animal Welfare Act and other federal statutes and regulations relating to animals and experiments involving animals and adhered to principles stated in the Guide for the Care and Use of Laboratory Animals (http://www.nap.edu/readingroom/books/labrats/chaps.html). The facility where this research was conducted is fully accredited by the Association for Assessment and Accreditation of Laboratory Animal Care International. The six media used for Bm cultures were Luria-Bertani broth (LB) (Difco), M9 supplemented with glucose at 0.5% (M9 glucose), M9 glucose with 0.5% liver infusion (Difco), 1% liver infusion, 1% liver infusion with limited O2 supply, 1% liver infusion with limited O2 supply and with 10 mM of the Ca2+ -chelating agent EGTA (Sigma-Aldrich, St. Louis, MO). Cultures were grown up to late-log phase (OD600 = 0.9 for M9; OD600 = 1.5 for media with liver infusion) at 37C with moderate shaking. Aliquots of cultures were withdrawn and rapidly mixed with 1.5 volumes of RNAprotect Bacteria Reagent (QIAGEN Inc., Valencia, CA) to prevent the degradation of RNA. Cells were immediately harvested and RNA prepared using the RNeasy kit (QIAGEN Inc., Valencia, CA) according the manufacturer's protocols.	Female BALB/c mice were obtained from Charles River Laboratories (National Cancer Institute, Frederick, MD) and were 6- to 8-weeks-old at the time of use. Three mice were injected intraperitoneally with 1.5 x 10<sup>7</sup> B. mallei ATCC 23344 (21 times the 50% lethal dose) and provided with rodent feed and water ad libitum and maintained on a 12-h light cycle. Two days postinfection the mice were euthanized in a CO2 chamber and spleens and livers were removed and homogenized in 1 ml of Trizol (Invitrogen Corp., Carlsbad, CA). The six media used for Bm cultures were Luria-Bertani broth (LB) (Difco), M9 supplemented with glucose at 0.5% (M9 glucose), M9 glucose with 0.5% liver infusion (Difco), 1% liver infusion, 1% liver infusion with limited O2 supply, 1% liver infusion with limited O2 supply and with 10 mM of the Ca2+ -chelating agent EGTA (Sigma-Aldrich, St. Louis, MO). Cultures were grown up to late-log phase (OD600 = 0.9 for M9; OD600 = 1.5 for media with liver infusion) at 37C with moderate shaking. Aliquots of cultures were withdrawn and rapidly mixed with 1.5 volumes of RNAprotect Bacteria Reagent (QIAGEN Inc., Valencia, CA) to prevent the degradation of RNA. Cells were immediately harvested and RNA prepared using the RNeasy kit (QIAGEN Inc., Valencia, CA) according the manufacturer's protocols.	RNA from the same organ types from three mice was pooled to compensate for potential individual variation. These pooled RNA samples, which contain both Bm and the host RNA, were used for the experiments without further purification of the Bm RNA, since RNA from uninfected mouse did not hybridize efficiently to the Bm microarray (data not shown). 	Two days postinfection the mice were euthanized in a CO2 chamber and spleens and livers were removed and homogenized in 1 ml of Trizol (Invitrogen Corp., Carlsbad, CA). RNA was purified following the recommended protocol from the manufacturer. Cultures were grown up to late-log phase (OD600 = 0.9 for M9; OD600 = 1.5 for media with liver infusion) at 37C with moderate shaking. Aliquots of cultures were withdrawn and rapidly mixed with 1.5 volumes of RNAprotect Bacteria Reagent (QIAGEN Inc., Valencia, CA) to prevent the degradation of RNA. Cells were immediately harvested and RNA prepared using the RNeasy kit (QIAGEN Inc., Valencia, CA) according the manufacturer's protocols.	Bm genomic DNA was prepared from an LB-grown Bm culture grown to mid-log phase (OD600 = 1.0) using DNeasy Tissue kit (QIAGEN Inc., Valencia, CA). 	Labeling was conducted following TIGR Standard operating procedure (SOP) #M004.2, which is available at http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml	Labeling was conducted following TIGR Standard operating procedure (SOP) #M004.2, which is available at http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml	Labeling was conducted following TIGR Standard operating procedure (SOP) #M004.2, which is available at http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml	Labeling was conducted following TIGR Standard operating procedure (SOP) #M004.2, which is available at http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml	Hybridization was conducted following TIGR SOP #M005.3, which is available at http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml	Differentially expressed genes at the 95% confidence level were determined using intensity-dependent Z-scores (with Z=1.96) as implemented in MIDAS. The resulting lists of the genes were examined further by cross comparison between experiments using TIGR MEV (http://www.tigr.org/software , TIGR, Rockville, MD) using Euclidean distance and hierarchical clustering with average linkage clustering method.
Protocol Parameters				Amplification;Extracted product;	Amplification;Extracted product;	Amount of nucleic acid labeled;Label used;Amplification;	Label used;Amplification;Amount of nucleic acid labeled;	Amount of nucleic acid labeled;Amplification;Label used;	Amplification;Label used;Amount of nucleic acid labeled;	Volume;temperature;Quantity of label target used;time;Chamber type;
Protocol Hardware
Protocol Software
Protocol Contact
Protocol Term Source REF			mo	mo	mo	mo	mo	mo	mo	mo	mo
SDRF File	E-MEXP-334.sdrf.txt
Term Source Name	mo		ArrayExpress	The MGED Ontology	mo	EFO
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php		http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/
Term Source Version