Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene Expression Circulating B Lymphocytes for Smoking Females

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Feng Pan

PROVIDER: E-GEOD-18723 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

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.

Pan Feng F Yang Tie-Lin TL Chen Xiang-Ding XD Chen Yuan Y Gao Ge G Liu Yao-Zhong YZ Pei Yu-Fang YF Sha Bao-Yong BY Jiang Yan Y Xu Chao C Recker Robert R RR Deng Hong-Wen HW

Immunogenetics 20100309 4

As pivotal immune guardians, 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 firstly compared the gene expression profiles of peripheral circulating B cells between 39 smoking and 40 non-smoking healthy US white women. A total of 125 differential expressed genes we ...[more]

PMID: 20217071

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Project description:Gastric cancer (GC) is one of the most common cancer worldwide. Specific and reliable molecular markers are limited; it is critical to identify new biomarkers for GC to aid in early diagnosis, treatment strategy, and prognosis evaluation. Microarray technology makes it possible to measure the expression levels of thousands of genes, and identifying meaningful and useful molecular targets from these large data. Total RNA was extracted from 10 pairs of GC tissue and adjacent non-tumor mucosa using TRIzolÂ® reagent (Invitrogen, Carlsbad, CA, US) following the manufacturer's instructions. The RNA integrity number (RIN), detected by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US), was used to determine the RNA integrity. Total RNA meeting the specified quality criteria (RIN â¥ 7.0 and 28S/18S â¥ 0.7) were further purified using an RNase-Free DNase Set (Qiagen, Hilden, Germany) and an RNeasyÂ® Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. Purified total RNA was then used for obtaining biotin-labeled cRNA by applying the GeneChipÂ® 3'IVT Express Kit (Affymetrix, Santa Clara, CA, US), according to the manufacturer's instructions. Then, the GeneChipÂ® Hybridization, Wash, and Stain Kit (Affymetrix, Santa Clara, CA, US) was used for performing the array hybridization and wash, with the use of a GeneChipÂ® Hybridization Oven 645 (Affymetrix, Santa Clara, CA, US) and a GeneChipÂ® Fluidics Station 450 (Affymetrix, Santa Clara, CA, US). All arrays were scanned using a GeneChipÂ® Scanner 3000 (Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with the default settings. Raw data were normalized by the MAS 5.0 algorithm in GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US). The significance analysis of microarray (SAM) was used to identify genes that were differentially expressed between the GC and normal tissues. Genes were considered to be differentially expressed when the Tumor versus Normal signal log ratio values were â¥2 or â¤0.5.

Dataset Information

Gene Expression Circulating B Lymphocytes for Smoking Females

Publications

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.

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