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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 10, 2020 |
| Title |
Blood, Smoker_2 |
| Sample type |
genomic |
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| Source name |
Blood
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| Organism |
Homo sapiens |
| Characteristics |
ethnicity: African-American
age: 42
gender: Male
cpd: 30
hsi: 5
ftnd: 9
smoking_status: Smoker
tissue: Blood
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| 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.
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| Label |
cy3, cy5
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| 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.
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| 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).
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| 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.
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| Description |
200027
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| 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)
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| Submission date |
Apr 09, 2020 |
| Last update date |
Apr 10, 2020 |
| Contact name |
Yi Xu |
| E-mail(s) |
xuyi714@126.com
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| Organization name |
The First Affiliated Hospital, Zhejiang University School of Medicine
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| Department |
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases
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| Street address |
No. 17, Dazhi Road, old Zhejiang, Shangcheng District
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310009 |
| Country |
China |
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| 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 |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM4463149_8378323056_R02C01_Grn.idat.gz |
2.2 Mb |
(ftp)(http) |
IDAT |
| GSM4463149_8378323056_R02C01_Red.idat.gz |
2.2 Mb |
(ftp)(http) |
IDAT |
| Processed data are available on Series record |
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