Comment[ArrayExpressAccession]	E-MTAB-979
Investigation Title	In vitro transcriptional profiling of dendritic cells treated with Denileukin diftitox (ONTAK)
Comment[Submitted Name]	In vitro transcriptional profiling of dendritic cells treated with Denileukin diftitox (ONTAK)
Experiment Description	In order to assess the transcriptional modifications of dendritic cells treated with Denileukin diftitox (ONTAK), we profiled the whole transcriptome of monocyte-derived dendritic cells (moDC) from blood of healthy volounteers after stimulation with a maturation cocktail with or without the addition of ONTAK.
Date of Experiment
Public Release Date	2013-09-04
Comment[AEExperimentType]	transcription profiling by array
Comment[AEExperimentDisplayName]	Transcription profiling by array of human monocyte-derived cells treated with Denileukin diftitox (ONTAK)
Experimental Design	compound treatment design
Experimental Design Term Accession Number	efo:EFO_0001755
Experimental Design Term Source REF	EFO
Experimental Factor Name	COMPOUND
Experimental Factor Type	compound
Experimental Factor Term Accession Number
Experimental Factor Term Source REF
Person First Name	Luca
Person Last Name	Beltrame
Person Mid Initials
Person Email	luca.beltrame@marionegri.it
Person Phone
Person Fax
Person Address
Person Affiliation
Person Roles	submitter
Person Roles Term Accession Number	efo:EFO_0001741
Person Roles Term Source REF	EFO
PubMed ID
Publication DOI	10.1182/blood-2012-09-456988 
Publication Author List	Andreas S. Baur, Manfred B. Lutz, Stephan Schierer, Luca Beltrame, Gabi Theiner, Elisabeth Zinser, Christian Ostalecki, Gordon Heidkamp, Ina Haendle, Michael Erdmann, Manuel Wiesinger, Waltraud Leisgang, Stefanie Gross, Ansgar J. Pommer, Eckhart Kämpgen, Diana Dudziak, Alexander Steinkasserer, Duccio Cavalieri, Beatrice Schuler-Thurner, and Gerold Schuler
Publication Title	Denileukin diftitox (ONTAK TM) induces a tolerogenic phenotype in dendritic cells and stimulates survival of resting Treg
Publication Status	submitted
Publication Status Term Accession Number
Publication Status Term Source REF
Protocol Name	P-MTAB-25284	P-MTAB-25285	P-MTAB-25286	P-MTAB-25287	P-MTAB-25288	P-MTAB-25289
Protocol Description	RNA was extracted using SuperAmp Lysis Buffer (Milteny Biotec) and purified using a SuperAmp Preparation Kit, according to the manufacturer's instructions.	PBMC from healthy volunteers were obtained following approval by the local ethics committee and informed consent. DC were generated from adherent, monocyte-enriched PBMC fractions by first exposing adherent, monocyte-enriched PBMC fractions to optimized concentrations of GM-CSF + IL-4 for 6 days to generate imDC, followed by addition of a maturation cocktail consisting of IL-1beta, IL-6, TNF- and PGE2 to harvest maDC on day 7.	The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays 4 x 44K using Agilent’s recommended hybridization chamber and oven.	250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.	Array files were pre-processed, removing probes flagged as unreliable by Agilent Feature Extraction software and summarizing multiple probes for the same gene to a single value. Background subtraction was performed according to the half method, followed by quantile normalization. The procedure was carried out with the Agi4x44PreProcess package, part of the Bioconductor software suite (http://www.bioconductor.org) using the R programming language (http://www.r-project.org).	Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies).
Protocol Type	RNA extraction	sample collection	nucleic acid hybridization	labeling	normalization data transformation	data acquisition
Protocol Term Accession Number	obo:OBI_0666666		obo:OBI_0302903	obo:OBI_0600038	obo:OBI_0200169	obo:OBI_0600013
Protocol Term Source REF	OBI		OBI	OBI	OBI	OBI
Protocol Parameters
Comment[Protocol Parameters Term Accession Number]
Comment[Protocol Parameters Term Source REF]
Term Source Name	CHEBI	EFO	NCBITaxon	NCIt	OBI
Term Source File	http://bioportal.bioontology.org/ontologies/46719	http://bioportal.bioontology.org/ontologies/46765	http://bioportal.bioontology.org/ontologies/38802	http://bioportal.bioontology.org/ontologies/46317
Term Source Version
SDRF File	E-MTAB-979.sdrf.txt