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Sample GSM4463150 Query DataSets for GSM4463150
Status Public on Apr 10, 2020
Title Blood, Smoker_3
Sample type genomic
 
Source name Blood
Organism Homo sapiens
Characteristics ethnicity: African-American
age: 32
gender: Female
cpd: 40
hsi: 6
ftnd: 9
smoking_status: Smoker
tissue: Blood
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from EDTA-treated peripheral venous blood of each subject using the Qiagen DNA purification kit. All DNA samples were treated with RNase A to remove potential contaminating RNA, and DNA quality and the concentration of each sample was determined by the A260/A280 absorbance ratio.
Label cy3, cy5
Label protocol The concentration of each DNA sample was first measured using the QuantiT™ dsDNA assay kit (Life Technologies, Carlsbad, CA) and then 50 DNA samples were pooled in equimolar amounts, as suggested by the manufacturers.
 
Hybridization protocol RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48 °C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).
Scan protocol All samples were genotyped using the Infinium Human Exome-12 v1.1 BeadChip (Illumina, Inc., San Diego, CA, USA) according to the manufacturer’s protocol.
Description 200028
Data processing After genotyping, we performed the following quality control analyses on all genotyped SNPs. First, among 242 901 genotyped variants, we excluded all insertions and deletions to ensure that all base pair positions were unique and referred to the same variant. Second, any SNP with a call rate of <95% was excluded. Third, we removed those SNPs that were not in Hardy–Weinberg equilibrium at a p value of < 1.0 × 10−6. Finally, we used a 5% minor allele frequency (MAF) as a threshold to define rare and common variants, and any SNP with an MAF of <0.05 was excluded from the analysis.
[value definition] Genotype: AA,AB,BB,or NC (no call)
 
Submission date Apr 09, 2020
Last update date Apr 10, 2020
Contact name Yi Xu
E-mail(s) xuyi714@126.com
Organization name The First Affiliated Hospital, Zhejiang University School of Medicine
Department State Key Laboratory for Diagnosis and Treatment of Infectious Diseases
Street address No. 17, Dazhi Road, old Zhejiang, Shangcheng District
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310009
Country China
 
Platform ID GPL18545
Series (1)
GSE148375 An Exome-Wide Association Study Identifies New Susceptibility Loci for the Risk of Nicotine Dependence in African-American Populations

Supplementary file Size Download File type/resource
GSM4463150_8378323056_R03C01_Grn.idat.gz 2.2 Mb (ftp)(http) IDAT
GSM4463150_8378323056_R03C01_Red.idat.gz 2.2 Mb (ftp)(http) IDAT
Processed data are available on Series record

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