Comment[ArrayExpressAccession]	E-GEOD-11095
Public Release Date	2008-05-29
Investigation Title	Dose response of carbon monoxide treatment of M. tuberculosis								
Comment[Submitted Name]	Dose response of carbon monoxide treatment of M. tuberculosis
Experiment Description	Transcriptional profiling of M. tuberculosis growing in log phase treated with various concentrations of carbon monoxide versus untreated controls Keywords: Dose response Two condition experiment, CO treated cells at 2000, 200 and 20 ppm versus untreated controls. Biological replicates: 2 replicates per dose, 1 array per replicate								
Date of Experiment									
Term Source Name	EFO
Term Source Version									
Term Source File	http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/efo.owl								
Person Last Name	Shiloh	Shiloh	Cox						
Person First Name	Michael	Michael	Jeffery						
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Person Email	michael.shiloh@ucsf.edu								
Person Affiliation	University of California at San Francisco								
Person Phone	415-476-5159								
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Person Address	University of California at San Francisco, 600 16th St. N376, San Francisco, CA, USA								
Person Roles	submitter								
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Protocol Name	P-GSE11095-1	P-GSE11095-6	P-GSE11095-3	P-GSE11095-9	P-GSE11095-8	P-GSE11095-7	P-GSE11095-2	P-GSE11095-4	P-GSE11095-5
Protocol Description	ID_REF = <br>VALUE = normalized log2 ratio 635/532 representing treated sample/untreated control	Cy5 and Cy3 labelled probes were mixed and hybridized to oligonucleotide MTB arrays (Operon Biosystems) at 63 C for 18h.After hybridization, slides were washed in batch.	M. tuberculosis growing in 7H9 with 0.2% Tween 80 in early log phase	Ratio-based normalization, flagged features using Spotreader default parameters	Data was acquired using Spotreader 1.3.1.0 and Acuity 4.0 software	Slides were scanned using an Axon 4000B scanner and GenePix software.	M. tuberculosis treated with 2000, 200, 20 or 0 ppm CO gas in the headspace for 48 hours.	RNA was extracted from 50 ml of culture by beadbeating in Trizol and RNA purified with Qiagen Rneasy columns per manufacturers instructions.	5 ug total RNA was reverse transcribed into cDNA using random hexamer primers in the presence of aa-dUTP. cDNA was labelled with Cy dyes (Amersham) and purified over Zymo DNA binding columns.
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Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling
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Publication Title	Mycobacterium tuberculosis senses host-derived carbon monoxide during macrophage infection.								
Publication Author List	Shiloh MU, Manzanillo P, Cox JS								
PubMed ID	18474359								
Publication DOI	10.1016/j.chom.2008.03.007								
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Comment[SecondaryAccession]	GSE11095								
Comment[GEOLastUpdateDate]	2009-10-29
Comment[AEExperimentType]	transcription profiling by array								
Comment[GEOReleaseDate]	2008-05-28
Comment[ArrayExpressSubmissionDate]	2008-04-07
SDRF File	E-GEOD-11095.sdrf.txt