Investigation Title Comparison of splenic and small intestine lamina propria dendritic cells Comment[Submitted Name] Comparison of splenic and small intestine lamina propria dendritic cells Experimental Design transcription profiling by array Experimental Design Term Source REF EFO Comment[SecondaryAccession] Comment[SecondaryAccession] GSE22136 Comment[ArrayExpressReleaseDate] 2010-06-16 Comment[AEMIAMESCORE] 4 Comment[ArrayExpressAccession] E-GEOD-22136 Comment[MAGETAB TimeStamp_Version] 2010-08-04 14:54:04 Last Changed Rev: 13058 Experimental Factor Name CELL TYPE Experimental Factor Type cell type Experimental Factor Term Source REF Person Last Name Nakaya Person First Name Helder Person Mid Initials I Person Email hnakaya@emory.edu Person Phone 1-404-712-2594 Person Fax Person Address Emory Vaccine Center, Emory University, 954 Gatewood Road, room 2040, Atlanta, Georgia, United States Person Affiliation Emory University Person Roles submitter Person Roles Term Source REF The MGED Ontology Quality Control Type Quality Control Term Source REF Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2010-06-16 PubMed ID Publication DOI Publication Author List Publication Title Publication Status Publication Status Term Source REF Experiment Description This SuperSeries is composed of the following subset Series: GSE22127: Expression profiling of small intestine lamina propria dendritic cells GSE22128: Expression profiling of splenic dendritic cells Dendritic cells play a vital role in initiating robust immunity against pathogens as well as maintaining immunological tolerance to self antigens, food antigens and intestinal commensals. However, the intracellular signaling networks that program DCs to become tolerogenic are largely unknown. To address this, we analyzed gene expression profiles using microarray analysis of purified intestinal lamina propria DCs (CD11c+ CD11b+ DCs and CD11c+ CD11b- DCs) and compared it to splenic DCs (CD11c+ DC), from mice. We sought to determine the unique genetic profile of small intestine lamina propria CD11c+ cells compared to splenic CD11c+ cells. We performed a meta-analysis using the expression profiles of Intestinal lamina propria CD11c+ CD11b+ DCs (GSM550122), Intestinal lamina propria CD11c+ CD11b- DCs (GSM550121) and Splenic CD11c+ DCs (GSM550126). This study combined and re-normalized the microarray data from GSE22127 and GSE22128 studies. Refer to individual Series for additional details Protocol Name P-GSE22136-2 P-GSE22136-7 P-GSE22136-8 P-GSE22136-3 P-GSE22136-4 P-GSE22136-5 P-GSE22136-6 P-GSE22136-1 Protocol Type nucleic_acid_extraction nucleic_acid_extraction nucleic_acid_extraction labeling hybridization image_aquisition feature_extraction bioassay_data_transformation Protocol Description CD11c+ CD11b- DCs were FACS-sorted and the RNA extracted using the Qiagen RNeasy Mini Kit protocol according to the manufacturer’s instructions. Samples were treated with DNase. CD11c+ CD11b+ DCs were FACS-sorted and the RNA extracted using the Qiagen RNeasy Mini Kit protocol according to the manufacturer’s instructions. Samples were treated with DNase. CD11c+ DCs were FACS-sorted and the RNA extracted using the Qiagen RNeasy Mini Kit protocol according to the manufacturer’s instructions. Samples were treated with DNase. As per Vanderbilt Microarray Shared Resource Standard Protocol As per Vanderbilt Microarray Shared Resource Standard Protocol As per Vanderbilt Microarray Shared Resource Standard Protocol RMA-normalized expression values were obtained for all probe sets using Expression Console software (Affymetrix Inc) ID_REF =
VALUE = RMA-normalized gene level expression values from Expression Console Protocol Parameters Protocol Hardware Protocol Software Protocol Contact Protocol Term Source REF The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology SDRF File E-GEOD-22136.sdrf.txt Term Source Name NCBI Taxonomy The MGED Ontology ArrayExpress EFO The MGED Ontology Term Source File http://www.ncbi.nlm.nih.gov/Taxonomy/ http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php Term Source Version