Comment[ArrayExpressAccession]	E-GEOD-38261
MAGE-TAB Version	1.1							
Public Release Date	2013-01-07
Investigation Title	Distinct Transcriptional Signatures of Bone Marrow-Derived C57BL/6 and DBA/2 Dendritic Leucocytes Hosting Live Leishmania amazonensis Amastigotes							
Comment[Submitted Name]	Distinct Transcriptional Signatures of Bone Marrow-Derived C57BL/6 and DBA/2 Dendritic Leucocytes Hosting Live Leishmania amazonensis Amastigotes
Experiment Description	To determine the modulation of gene expression of  C57BL/6 and DBA/2 BMDLs in the presence of living intracellular Leishmania amazonensis amastigotes A genome-wide transcriptional analysis was performed by comparing the gene expression profiles of control DLs and live amastigote-hosting DLs from both mouse strains. Dendritic Leucocytes were generated in vitro from bone marrow progenitors (C57Bl/6 and DBA/2 mice). Leishmania amazonensis amastigotes were purified from mouse cutaneous lesions and were added to DL cultures. After 24h, and following a sorting procedure, only BMDls housing living amastigotes were selected for total RNA extraction. Three Biological replicates per condition were run.							
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	Lang	Lang	de la Llave	Lecoeur	Soubigou	Coppée	Milon	Prina
Person First Name	Thierry	Thierry	Emilie	Hervé	Guillaume	Jean-Yves	Geneviève	Eric
Person Email	thierry.lang@pasteur.fr							
Person Affiliation	Institut Pasteur							
Person Phone	+33145688673							
Person Fax	+331 45 688332							
Person Address	parasitology and Mycology, Institut Pasteur, 25 rue du Dr Roux , Paris, France							
Person Roles	submitter							
Protocol Name	P-GSE38261-1	P-GSE38261-6	P-GSE38261-3	P-GSE38261-8	P-GSE38261-7	P-GSE38261-2	P-GSE38261-4	P-GSE38261-5
Protocol Description	ID_REF =  VALUE = Log2 RMA signal	See standard Affymetrix protocols	DLs were differentiated from bone marrow cells of DBA/2 or C57BL/6 mice.On day 4 post the distribution of DLs in the 6 well plate culture, DLs were exposed to freshly isolated DsRed2-LV79 amastigotes.	Gene-level expression values were derived from the CEL file probe-level hybridization intensities using the model-based Robust Multichip Average algorithm (RMA) (Bolstad et al., 2003). RMA performs normalization, background correction and data summarization. An analysis is performed using the LPE test (Jain, 2003) to identify significant differences in gene expression between parasite-free and parasite-harbouring DLs, and a p-value threshold of p < 0.05 is used as the criterion for significant differential expression. The estimated false discovery rate (FDR) was calculated using the Benjamini and Hochberg approach (Benjamini et al., 1995) in order to correct for multiple comparisons.	Following hybridization, the arrays were stained and scanned at 532 nm using an Affymetrix GeneChip Scanner 3000 which generates individual CEL files for each array.	L. amazonensis amastigote-hosting DLs were sorted by selecting cells expressing both surface MHC Class II molecules and DsRed2 fluorescence and immediately used for further studies.	Mouse total RNA was extracted from either MHC class II+ BMD-DLs using the RNeasy Plus Mini-Kit (Qiagen).The quality control (QC) and concentration of RNA were determined using the NanoDrop ND-1000 micro-spectrophotometer and the Agilent-2100 Bioanalyzer.	Two hundred ng of total RNA per sample were processed, labelled and hybridized to Affymetrix Mouse Gene ST 1.0 arrays, following Affymetrix Protocol (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf).
Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling
Experimental Factor Name	STRAIN OR LINE	INFECTIOUS AGENT						
Experimental Factor Type	strain or line	infectious agent						
Publication Title	Distinct Transcriptional Signatures of Bone Marrow-Derived C57BL/6 and DBA/2 Dendritic Leucocytes Hosting Live Leishmania amazonensis Amastigotes.							
Publication Author List	Giraud E, Lecoeur H, Soubigou G, Copp�e JY, Milon G, Prina E, Lang T							
PubMed ID	23272268							
Publication DOI	10.1371/journal.pntd.0001980							
Comment[SecondaryAccession]	GSE38261							
Comment[GEOReleaseDate]	2013-01-07							
Comment[ArrayExpressSubmissionDate]	2012-05-25							
Comment[GEOLastUpdateDate]	2013-01-09							
Comment[AEExperimentType]	transcription profiling by array							
Comment[AdditionalFile:Data1]	GSE38261_Analysis_results.xls							
SDRF File	E-GEOD-38261.sdrf.txt