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| Status |
Public on May 20, 2017 |
| Title |
saliva derived genomic DNA [SA064]_SNP_genotype |
| Sample type |
genomic |
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| Source name |
Oragene saliva
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| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 71
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extracted from saliva sampled using Oragene kits by DNA Genotek using PrepIT reagent and a standard protocol
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| Label |
biotin
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| Label protocol |
standard Illumina protocol
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| Hybridization protocol |
genomic DNA was amplified, fragmented and hybridised to Illumina OmniExpress, OmniExpress Plus, and HumanHap550 arrays using standard Illumina protocol
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| Scan protocol |
chips were scanned using an Illumina iScan and recommended settings
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| Description |
saliva sample
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| Data processing |
genotypes were oriented to the hg19 build, filtered for quality and missingness, and merged with other datasets to yield a final set of 298346 SNPs which were used for all analyses in the study. PLINK software was used for analysis.
The .bim file contains positional information about each SNP. It has 6 columns: chromosome, rsID or other identifier, genetic distance in morgans, physical distance in base pairs, and two columns with the alleles.
The .fam file contains information about the individuals. It has 6 columns: family ID, individual ID, paternal ID, maternal ID, sex, and phenotype. The parental IDs are unknown for these individuals, so these columns are set to 0 for all. There is also no relevant phenotype for these individuals, so this column is set to -9 for all.
The .bed.data file contains the information about each SNP for each individual encoded in binary format.
The .map file contains the same data as the .bim file except that it does not contain last two columns with the specific alleles.
The .ped file is the same as the .fam file except it contains additional columns, two for every SNP position, which contain the genotypes.
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| Submission date |
May 19, 2017 |
| Last update date |
May 20, 2017 |
| Contact name |
Shyamalika Gopalan |
| E-mail(s) |
shyamalika.gopalan@stonybrook.edu
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| Organization name |
Stony Brook University
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| Street address |
100 Nicolls Road
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| City |
Stony Brook |
| ZIP/Postal code |
11794 |
| Country |
USA |
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| Platform ID |
GPL18900 |
| Series (2) |
| GSE99090 |
SNP genotyping of ǂKhomani San |
| GSE99091 |
Genome-wide DNA methylation and SNP genotyping of ǂKhomani San |
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| Supplementary data files not provided |
| Processed data are available on Series record |
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