Comment[ArrayExpressAccession]	E-GEOD-57124
MAGE-TAB Version	1.1						
Public Release Date	2014-12-21
Investigation Title	Lung-resident myeloid-derived suppressor cells display dual functionality in experimental tuberculosis						
Comment[Submitted Name]	Lung-resident myeloid-derived suppressor cells display dual functionality in experimental tuberculosis
Experiment Description	Using cell-based approaches and experimental mouse models for pulmonary TB we unveiled MDSCs as new myeloid populations directly interacting with Mycobacterium tuberculosis (Mtb). MDSCs readily phagocytosed Mtb, released proinflammatory (IL-6, IL-1M-NM-1) and immunomodulatory (IL-10) cytokines while retaining their suppressive capacity. MDSCs were identified at the site of infection in disease-resistant and -susceptible mice during pulmonary TB. Excessive MDSC accumulation in lungs correlated with elevated surface expression of IL-4RM-NM-1 and heightened TB lethality. Microarray experiments were performed as dual-color hybridizations on Agilent mouse whole genome catalog 44K arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.						
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	Mollenkopf	Knaul	Mollenkopf	Kaufmann	Dorhoi		
Person First Name	Hans-Joachim	Julia	Hans-Joachim	Stefan	Anca		
Person Mid Initials		K		H			
Person Email	mollenkopf@mpiib-berlin.mpg.de						
Person Affiliation	Max-Planck-Institute for Infection Biology						
Person Phone	+49 30 28460 482						
Person Address	Max-Planck-Institute for Infection Biology, CharitM-CM-)platz 1, Berlin, Germany						
Person Roles	submitter						
Protocol Name	P-GSE57124-1	P-GSE57124-5	P-GSE57124-6	P-GSE57124-2	P-GSE57124-3	P-GSE57124-4	P-GSE57124-7
Protocol Description	Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware) ID_REF =  VALUE = LogRatio (base 10) of Cy5/Cy3 intensities	RNA labeling was performed with the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according supplier's instructions.	Whole mouse genome 44k microarrays were done according to the supplierM-bM-^@M-^Ys protocol (Agilent Technologies) using the SSC wash protocol	Mice were aerosol-infected with 100M-bM-^@M-^S200 colony forming units (CFU)/mouse Mtb (strain H37Rv) using a Glas-Col inhalation system. RNA from five pooled lung homogenates were prepared as previously described (Dorhoi et al., The adaptor molecule card9 is essential for tuberculosis control. The Journal of experimental medicine 2010;207:777-792)	TB-resistant C57BL/6 (Charles River) or -susceptible 129S2 mice (129SvPas (22), aged 8-12 weeks and housed under SPF conditions at the Max Planck Institute for Infection Biology (Berlin, Germany). M.tuberculosis H37Rv were grown to mid-log phase in Middlebrook 7H9 broth (BD Biosciences) supplemented with 10% ADC enrichment (BD Biosciences), 0.05% glycerol and Tween 80.	Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturerM-4s protocol.	Scanning of microarrays was performed with 5 M-5m resolution using a DNA microarray laser scanner (Agilent Technologies)
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	strain	time					
Experimental Factor Type	strain	time					
Publication Title	Lung-residing myeloid-derived suppressors display dual functionality in murine pulmonary tuberculosis.						
Publication Author List	Knaul JK, JM-oM-?M-=rg S, Oberbeck-Mueller D, Heinemann E, Scheuermann L, Brinkmann V, Mollenkopf HJ, Yeremeev V, Kaufmann SH, Dorhoi A						
PubMed ID	25275852						
Publication DOI	10.1164/rccm.201405-0828OC						
Comment[SecondaryAccession]	GSE57124						
Comment[GEOReleaseDate]	2014-12-21						
Comment[ArrayExpressSubmissionDate]	2014-04-28						
Comment[GEOLastUpdateDate]	2014-12-23						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-57124.sdrf.txt