Comment[ArrayExpressAccession]	E-GEOD-27984
MAGE-TAB Version	1.1							
Public Release Date	2012-09-19
Investigation Title	PPD stimulated PBMCs from tuberculosis patients, latent infectious individuals and healthy controls.							
Comment[Submitted Name]	PPD stimulated PBMCs from tuberculosis patients, latent infectious individuals and healthy controls.
Experiment Description	Comprehensively compare the transcriptional difference in PPD stimulated PBMCs from individuals with different tuberculosis infectious status: tuberculosis patients, latent infectious individuals and healthy controls using the microarray analysis. Two-condition experiment, PBMCs vs. PPD-PBMCs. 12 individuals: 4 TB patients, 4 latent infectious individuals and 4 healthy controls.							
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	Lu	Lu	Zhang					
Person First Name	Chanyi	Chanyi	Wenhong					
Person Email	yanzi.mutou@yahoo.com.cn							
Person Affiliation	Fudan University							
Person Phone	86-15921587656							
Person Address	Fudan University, 220 Handan Rd, Shanghai, China							
Person Roles	submitter							
Protocol Name	P-GSE27984-1	P-GSE27984-6	P-GSE27984-3	P-GSE27984-8	P-GSE27984-7	P-GSE27984-2	P-GSE27984-4	P-GSE27984-5
Protocol Description	ID_REF =  VALUE = normalized log2 ratio (Cy3/Cy5) representing stimulated/unstimulated	Each Slide was hybridized with 825ng Cy3-labeled cRNA and 825ng Cy-5 labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US)in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US)with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.	PBMCs were cultured with AIM-V (Invitrogen Life Technologies, USA) containing 2 mM L-glutamine, 50 ug/ml streptomycin sulfate, and 10 ug/ml gentamicin.	Raw data were normalized by Lowess(locally weighted scatter plot smoothing) algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).	Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.	10 ug/ml Mycobacterium tuberculosis purified protein derivative (PPD, Mycos Research LLC, Loveland, CO) treated or untreated for 4 hours before RNA extraction.	Total RNA extracted using Trizol following manufacturer's instructions	Total RNA were amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX, US), Cy3 NHS ester (Cat#PA13105, GE healthcare Biosciences, Pittsburgh, PA, US) ，Cy5 NHS ester (Cat#PA15100, GE healthcare Biosciences, Pittsburgh, PA, US)followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).
Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling
Experimental Factor Name	INFECTION STATUS							
Experimental Factor Type	infection status							
Publication Title	Novel biomarkers distinguishing active tuberculosis from latent infection identified by gene expression profile of peripheral blood mononuclear cells.							
Publication Author List	Lu C, Wu J, Wang H, Wang S, Diao N, Wang F, Gao Y, Chen J, Shao L, Weng X, Zhang Y, Zhang W							
PubMed ID	21904626							
Publication DOI	10.1371/journal.pone.0024290							
Comment[SecondaryAccession]	GSE27984							
Comment[GEOReleaseDate]	2012-09-19							
Comment[ArrayExpressSubmissionDate]	2011-03-16							
Comment[GEOLastUpdateDate]	2012-09-19							
Comment[AEExperimentType]	transcription profiling by array							
SDRF File	E-GEOD-27984.sdrf.txt