Comment[ArrayExpressAccession]	E-GEOD-18723
Public Release Date	2009-12-25
Investigation Title	Gene Expression Circulating B Lymphocytes for Smoking Females					
Comment[Submitted Name]	Gene Expression Circulating B Lymphocytes for Smoking Females
Experiment Description	B cells were found to be directly associated with the onset and development of many smoking-induced diseases. However, the in vivo molecular response of B cells underlying the female cigarette smoking remains unknown. Using the genome-wide Affymetrix HG-133A GeneChip® microarray, we compared the gene expression profiles of peripheral circulating B cells between 39 smoking and 40 non-smoking healthy US white females. B cells were isolated from 70 ml of whole blood from each subject using B cell positive isolation method (Dynabeads CD19,Pan B) from Invitrogen Life Technologies Dynal Biotech Inc,CA. Total RNA was extracted from B cells using Qiagen RNeasy Mini Kit. A total of 4ug total RNA was used to produced targets for each subject according to standard Affymetrix procedures. Hybridization was made for each subject. Multiple analytic approaches including mas5.0 algorithm (Affymetrix, Santa Clara, CA, USA), RMA (Robust Multiarray Algorithm), GCRMA (the improved GC-content adjusted RMA), and dChip were used for converting and normalizing our raw probe data to gene expression values Comparison was performed between smoking and non-smoking groups using t-test under Benjamini and Hochberg (BH) procedure mutiple-testing adjustment.					
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Term Source Name	EFO
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Term Source File	http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/efo.owl					
Person Last Name	Pan					
Person First Name	Feng					
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Person Email	panbaby@gmail.com					
Person Affiliation	Xi'an Jiaotong University					
Person Phone	008613601860460					
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Person Address	School of life science and technology, Xi'an Jiaotong University, Xian Ning West Road 28, Xi'an, Shaanxi, China					
Person Roles	submitter					
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Protocol Name	P-GSE18723-1	P-GSE18723-5	P-GSE18723-4	P-GSE18723-2	P-GSE18723-3	P-GSE18723-6
Protocol Description	ID_REF = <br>VALUE = MAS 5 signal<br>RMA = <br>GCRMA = <br>dChip = 	We use the Affymetrix Microarray Scanner by Hewlett-Packard 2500 and Microarray Suite 5.0 software for chip scanning and raw image generating.	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.	Seventy milliliters of blood were drawn from each recruited female. B cell isolation from 70 ml whole blood was performed using a positive isolation method with Dynabeads® CD19 (Pan B) and DETACHaBEAD® CD19 (Dynal Biotech, Lake Success, NY, USA) following the manufacturer’s protocols. B cell purity was assessed by flow cytometry (BD Biosciences, San Jose, CA USA) with fluorescence labeled antibodies, PE-CD19 and FITC-CD45. The average purity was 96.3% with less than 1% deviation.	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).	Microarray Suite 5.0 (MAS 5.0, Affymetrix, Santa Clara, CA, USA) software was used to generate array raw data in CEL files. A preselecting procedure adopted by our previous study (Xiao et al. 2008) was also used here. We selected a subset of 7,215 probe sets from a total of 22,283 for ~14,500 genes in the HG-133A array. Subsequent data analyses were performed on these selected probe sets. We applied multiple analytic approaches including mas5.0 algorithm (Affymetrix, Santa Clara, CA, USA), RMA (Robust Multiarray Algorithm), GCRMA (the improved GC-content adjusted RMA), and dChip for converting and normalizing our raw probe data to gene expression values.  Genes expressed differentially as determined by consensus using the 4 methods were extracted.
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Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	nucleic_acid_extraction	labeling	feature_extraction
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Experimental Factor Name	MENOPAUSAL	SMOKING	AGE			
Experimental Factor Type	menopausal	smoking	age			
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Publication Title	Impact of female cigarette smoking on circulating B cells in vivo: the suppressed ICOSLG, TCF3, and VCAM1 gene functional network may inhibit normal cell function.					
Publication Author List	Pan F, Yang TL, Chen XD, Chen Y, Gao G, Liu YZ, Pei YF, Sha BY, Jiang Y, Xu C, Recker RR, Deng HW					
PubMed ID	20217071					
Publication DOI	10.1007/s00251-010-0431-6					
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Comment[SecondaryAccession]	GSE18723					
Comment[GEOLastUpdateDate]	2010-03-18
Comment[AEExperimentType]	transcription profiling by array					
Comment[GEOReleaseDate]	2009-12-25
Comment[ArrayExpressSubmissionDate]	2009-10-22
SDRF File	E-GEOD-18723.sdrf.txt