Comment[ArrayExpressAccession]	E-MEXP-3408
Investigation Title	Transcription profiling of intramacrophage Burkholderia cenocepacia K56-2
Comment[Submitted Name]	Transcription profiling of intramacrophage Burkholderia cenocepacia K56-2
Comment[AEExperimentDisplayName]	Transcription profiling of intramacrophage Burkholderia cenocepacia K56-2
Comment[MIAMExpressLogin]	jtolman
Comment[MIAMExpressSubmissionID]	7875
Experiment Description	Effect of internalization by macrophages on bacterial gene transcription in Burkholderia cenocepacia
Experimental Design	reference_design	co-expression_design	stimulus_or_stress_design	replicate_design
Comment[AEExperimentType]	transcription profiling by array
Experimental Factor Name	TREATMENT
Experimental Factor Type	treatment
Person Last Name	Tolman	Valvano
Person First Name	Jennifer	Miguel
Person Email	jtolman2@uwo.ca	Miguel.Valvano@schulich.uwo.ca
Person Phone	519-661-3433	519-661-2111
Person Affiliation	University of Western Ontario	University of Western Ontario
Person Address	Microbiology and Immunology, Dental Sciences Building 3014, London, Ontario, N6A 5C1, Canada	Microbiology and Immunology, Dental Sciences Building 3014, London, Ontario, N6A 5C1, Canada
Person Roles	submitter	submitter
Person Roles Term Source REF	MGED Ontology	MGED Ontology
Quality Control Type	biological_replicate
Public Release Date	2011-12-07
Comment[ArrayExpressSubmissionDate]	2011-10-26 19:01
Publication Status	not yet submitted
Protocol Name	P-MTAB-23424	P-MTAB-23426	P-MTAB-23428	P-MTAB-23423	P-MTAB-23422
Protocol Description	cDNA was labelled with Cy5 using random nonamer primers and the CyScribe Array CGH Labeling Kit (GE Healthcare).  B. cenocepacia J2315 genomic DNA was labelled with Cy3 using the same method. (Parameters: Amplification = none, Mass unit = Micro gram)	Macrophages were infected with bacteria at a multiplicity of infection of 50:1.  Infection continued for 4 hours in DMEM-10% FBS at 37C in a 95% humidified atmosphere with 5% carbon dioxide.  At the conclusion of the infection, macrophage monolayers were washed and lysed with cold deionized water, and intracellular bacteria collected.	Bacteria lysed in 1 mg/mL lysozyme.  RNA extracted with TRIzol according to the manufacturer's instructions.  RNA treated with DNase.  RNA reverse-transcribed to cDNA, and microbial transcripts purified and amplified using selective capture of transcribed sequences (Daigle et al., Methods Enzymol., 2002).  (Parameters: Extracted product = total_RNA, Amplification = OTHER: SCOTS)	Bacteria were grown 16h, washed twice with DMEM-10% FBS, and resuspended in DMEM-10% FBS prior to determining OD600. (Parameters: start time = 16, time unit = hours, min temperature = 37, temperature unit = C, media = LB)	Equivalent numbers of bacteria (to those used to infect macrophages for intracellular bacteria) were maintained in DMEM-10% FBS at 37C in a 95% humidified atmosphere with 5% carbon dioxide.  After four hours, bacteria were resuspended and collected.
Protocol Type	labeling	specified_biomaterial_action	nucleic_acid_extraction	grow	specified_biomaterial_action
Protocol Term Source REF	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology
Term Source Name	MGED Ontology	ArrayExpress
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress/
SDRF File	E-MEXP-3408.sdrf.txt
PubMed ID	22321740
Publication Author List	Tolman JS, Valvano MA.
Publication Title	Global changes in gene expression by the opportunistic pathogen Burkholderia cenocepacia in response to internalization by murine macrophages.
Publication DOI	10.1186/1471-2164-13-63