Comment[ArrayExpressAccession]	E-GEOD-25913
Public Release Date	2011-05-01
Investigation Title	Gene expression profiling of the classical (CD14++CD16-), intermediate (CD14++CD16+) and nonclassical (CD14+CD16+) human monocyte subsets							
Comment[Submitted Name]	Gene expression profiling of the classical (CD14++CD16-), intermediate (CD14++CD16+) and nonclassical (CD14+CD16+) human monocyte subsets
Experiment Description	The new official nomenclature subdivides human monocytes into three subsets, classical (CD14++CD16-), intermediate (CD14++CD16+) and nonclassical (CD14+CD16+). Here, we comprehensively define relationships and unique characteristics of the three human monocyte subsets using microarray and flow cytometry analysis. Our analysis revealed that the intermediate and nonclassical monocyte subsets were most closely related. For the intermediate subset, majority of genes and surface markers were expressed at an intermediary level between the classical and nonclassical subset. There features therefore indicate a close and direct lineage relationship between the intermediate and nonclassical subset. From gene expression profiles, we define unique characteristics for each monocyte subset. Classical monocytes were functionally versatile, due to the expression of a wide range of sensing receptors and several members of the AP-1 transcription factor family. The intermediate subset was distinguished by high expression of MHC class II associated genes. The nonclassical subset were most highly differentiated and defined by genes involved in cytoskeleton rearrangement that explains their highly motile patrolling behavior in vivo. Additionally, we identify unique surface markers, CLEC4D, IL-13RA1 for classical, GFRA2, CLEC10A for intermediate and GPR44 for nonclassical. Our study hence defines the fundamental features of monocyte subsets necessary for future research on monocyte heterogeneity. Three human monocyte subsets, the CD14++CD16- classical, the CD14++CD16+ intermediate and CD14+CD16+ nonclassical subsets were purified using fluorescence activated cell sorting from peripheral blood mononuclear cells. RNA was processed from the three monocyte subsets from 4 individual donors in duplicates, giving a total of 24 samples.							
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Term Source Name	EFO
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Term Source File	http://bar.ebi.ac.uk:8080/trac/browser/branches/curator/ExperimentalFactorOntology/ExFactorInOWL/currentrelease/eforelease/efo.owl							
Person Last Name	Wong	Wong	Tai	Yeap	Wong	Han	Kourilsky	Wong
Person First Name	Kok Loon	Kok	Jing	Wei	Wing	Hao	Philippe	Siew
Person Mid Initials		L	Y	H	C			C
Person Email	wong_kok_loon@immunol.a-star.edu.sg							
Person Affiliation	A*STAR							
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Person Address	A*STAR, 8A Biomedical Grove, Biopolis, Singapore, Singapore							
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Protocol Name	P-GSE25913-1	P-GSE25913-6	P-GSE25913-5	P-GSE25913-2	P-GSE25913-3	P-GSE25913-4	P-GSE25913-7	
Protocol Description	ID_REF = <br>VALUE = Quantile and scaling method normalized signal intensity<br>Detection_Pval = 	Standard Illumina scanning protocol	Standard Illumina hybridization protocol	Classical (CD14++CD16-), intermediate (CD14++CD16+) and nonclassical (CD14+CD16+) monocyte subsets purified using fluorescence activated cell sorting based on relative CD14 and CD16 expression	RNA was isolated using Trizol extraction followed by Qiagen RNeasy mini kit according to the manufacturer's protocol. RNA quality was confirmed using the Agilent 2100 Bioanalyser.	Using Illumina® TotalPrep RNA Amplification Kit according to the manufacturer's protocol.	A quantile normalization variant was applied to the duplicates profiles, followed by the scaling method applied across all profiles to equalize medians readings. The data processing software is an in-house developed Matlab code. This method is elaborated in this published report &quot;Wong WC, Loh M, Eisenhaber F. On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation. Biol Direct. 2008 Jun 3;3:23.&quot; (PMID: 18522715).	
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Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	specified_biomaterial_action	nucleic_acid_extraction	labeling	feature_extraction	
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Experimental Factor Name	DONOR	MONOCYTE SUBSET	REP					
Experimental Factor Type	donor	monocyte subset	rep					
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Comment[SecondaryAccession]	GSE25913							
Comment[GEOLastUpdateDate]	2011-05-01
Comment[AEExperimentType]	transcription profiling by array							
Comment[GEOReleaseDate]	2011-04-30
Comment[ArrayExpressSubmissionDate]	2010-12-08
SDRF File	E-GEOD-25913.sdrf.txt