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| Status |
Public on Jun 03, 2022 |
| Title |
Hospitalized_COVID-19 [COV016] |
| Sample type |
genomic |
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| Source name |
Hospitalized for COVID-19
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| Organism |
Homo sapiens |
| Characteristics |
gender: female
age: 45.00
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the automated MagPurix 12 system according to the manufacturer’s protocol. DNA was quantified using the DS-11 Series of Spectrophotometer/Fluorometer (DeNovix).
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| Label |
cy3,cy5
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| Label protocol |
DNA was extracted using the automated MagPurix 12 system according to the manufacturer’s protocol. DNA was quantified using the DS-11 Series of Spectrophotometer/Fluorometer (DeNovix).
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| Hybridization protocol |
Genotyping was performed using the Infinium Global Screening Array-24 v3.0 BeadChip (Illumina, Inc., San Diego, CA, USA) according to the manufacturer’s protocol, which contained 654,027 genetic markers and developed by Avera Institute for Huma Genetics (South Dakota, USA). The Infinium Global Screening Array-24 v3.0 BeadChip would be best suited for this ethnically diverse cohort because it features a broad spectrum of diverse exonic content, including both cross population and population specific markers (EUR: 52,980 markers; EAS: 31,375 markers; AMR: 45,977 markers; AFR: 43,122 markers; SAS: 40,298 markers).
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| Scan protocol |
PLINK (version 1·9), R (version 3·4), SPSS (version 16·0), Haploview Software (version 4.2).
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| Data processing |
The matrix processed and matrix signal intensity files form Genome studio are uploaded.
The statistical analysis was conducted as a case-control panel, with controls characterized as non-hospitalized symptoms and cases characterized as hospitalized symptoms. Case-control association tests of the genotyped and imputed SNPs in the cohort were performed using PLINK (logistic regression). Two different analysis including covariates from the PCA without 1000 Genomes reference samples were run to control for potential population stratification (analysis I), as well as population stratification, age, and gender effects (analysis II).
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| Submission date |
Sep 15, 2021 |
| Last update date |
Jun 03, 2022 |
| Contact name |
Habiba Alsafar |
| Organization name |
Khalifa University
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| Department |
Center of Biotechnology
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| Street address |
Al Saada St. Muroor Road
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| City |
Abu Dhabi |
| ZIP/Postal code |
127788 |
| Country |
United Arab Emirates |
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| Platform ID |
GPL23391 |
| Series (1) |
| GSE184150 |
Genome-Wide Association Study of Hospitalized COVID-19 Patients in the United Arab Emirates |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM5578599_204433830043_R02C01_Grn.idat.gz |
4.9 Mb |
(ftp)(http) |
IDAT |
| GSM5578599_204433830043_R02C01_Red.idat.gz |
5.0 Mb |
(ftp)(http) |
IDAT |
| Processed data are available on Series record |
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