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Sample GSM2632140 Query DataSets for GSM2632140
Status Public on May 20, 2017
Title saliva derived genomic DNA [SA029]_SNP_genotype
Sample type genomic
 
Source name Oragene saliva
Organism Homo sapiens
Characteristics gender: male
age: 60
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
Label biotin
Label protocol standard Illumina protocol
 
Hybridization protocol genomic DNA was amplified, fragmented and hybridised to Illumina OmniExpress, OmniExpress Plus, and HumanHap550 arrays using standard Illumina protocol
Scan protocol chips were scanned using an Illumina iScan and recommended settings
Description saliva sample
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.
 
Submission date May 19, 2017
Last update date May 20, 2017
Contact name Shyamalika Gopalan
E-mail(s) shyamalika.gopalan@stonybrook.edu
Organization name Stony Brook University
Street address 100 Nicolls Road
City Stony Brook
ZIP/Postal code 11794
Country USA
 
Platform ID GPL6982
Series (2)
GSE99090 SNP genotyping of ǂKhomani San
GSE99091 Genome-wide DNA methylation and SNP genotyping of ǂKhomani San

Supplementary data files not provided
Processed data are available on Series record

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