Comment[ArrayExpressAccession]	E-GEOD-39606
MAGE-TAB Version	1.1					
Public Release Date	2013-07-23
Investigation Title	Gene expression data in CD4+ and CD8+ cells in sarcoidosis patients following antimycobacterial therapy					
Comment[Submitted Name]	Gene expression data in CD4+ and CD8+ cells in sarcoidosis patients following antimycobacterial therapy
Experiment Description	Many chronic cutaneous diseases associated with microbial antigens demonstrate clinical progression due to T cell hyporesponsiveness. Appropriate antimicrobial therapy restores T cell function, leading to clinical resolution.  Due to the association of sarcoidosis with mycobacterial antigens, we compared the efficacy of antimycobacterial therapy with placebo in chronic cutaneous sarcoidosis. We conducted a randomized, placebo-controlled, single-blind trial on chronic cutaneous sarcoidosis subjects.  Participants received the oral CLEAR regimen:  Levofloxacin 750 mg on day 1, then 500 mg daily, Ethambutol 1200 mg daily, Azithromycin 500 mg on day 1, then 250 mg daily, and Rifampin 300 mg daily, or a comparative placebo regimen, for a total of 8 weeks, with a 180 day follow-up.  Participants were monitored for absolute change in lesion diameter and decrease in granulomas burden upon completion of therapy.					
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	Pandit	Pandit	Drake	Kaminski		
Person First Name	Kusum	Kusum	Wonder	Naftali		
Person Mid Initials	Vijay	V				
Person Email	panditkv@upmc.edu					
Person Affiliation	University of Pittsburgh					
Person Phone	412-624-9046					
Person Fax	412-383-8864					
Person Address	Medicine-PACCM, University of Pittsburgh, 200, Lothrop street, W1200-25A Biomedical Science Tower, Pittsburgh, PA, USA					
Person Roles	submitter					
Protocol Name	P-GSE39606-1	P-GSE39606-4	P-GSE39606-5	P-GSE39606-2	P-GSE39606-3	P-GSE39606-6
Protocol Description	The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters. ID_REF =  VALUE = Cyclic lowess normalized signal intensity	Cy3 labeled RNA was prepared according to the standard Agilent protocol from 50ng total RNA	Labeled RNA was hybridized for 17 hr at 65C on Agilent 8X60K microRNA array. Arrays were washed according to the manufacturer's protocol.	Participants received the oral CLEAR regimen: Levofloxacin 750 mg on day 1, then 500 mg daily, Ethambutol 1200 mg daily, Azithromycin 500 mg on day 1, then 250 mg daily, and Rifampin 300 mg daily, or a comparative placebo regimen, for a total of 8 weeks, with a 180 day follow-up.	Total RNA extracted using miRNeasy mini kit (Qiagen) according to the manufacturer's instructions.	Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60K array slides
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	CELL TYPE					
Experimental Factor Type	cell type					
Comment[SecondaryAccession]	GSE39606					
Comment[GEOReleaseDate]	2013-07-23					
Comment[ArrayExpressSubmissionDate]	2012-07-24					
Comment[GEOLastUpdateDate]	2013-07-24					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-39606.sdrf.txt