NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM739549 Query DataSets for GSM739549
Status Public on Jun 09, 2011
Title Mesoamerican Totonac male F038958
Sample type genomic
 
Source name Mesoamerican Totonac male
Organism Homo sapiens
Characteristics cell type: buccal cell
lab id: F038958
population: Totonac
clade: C1b
polymorphisms relative to rcrs: 16223T, 16298C, 16325C, 16327T, 72C, 73G, 246C, 249d, 263G, 290d, 291d, 309.1C, 315.1C, 489C, 493G, 523d, 524d
gender: male
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from blood or mouthwash sample using standard protocols.
Label Biotin
Label protocol standard Affymetrix protocol
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description saliva
Hybridized to 6.0 chip
Data processing CEL files were processed using Birdseed version 2 in the Affymetrics Power Tools package.
Standard genotype calls with missing data or no call represented by blanks (NN). Important note: Calls were based on an early version of the Affymetrix annotation file. Therefore some AT and GC SNPs will be strand reversed relative to the current hg19 build.
 
Submission date Jun 08, 2011
Last update date Jun 09, 2011
Contact name Scott Watkins
E-mail(s) scott.watkins@genetics.utah.edu
Phone 801-585-3385
Fax 801-585-9148
Organization name University of Utah
Department Human Genetics
Street address 15 N 2030 E Rm2100
City Salt Lake City
State/province UT
ZIP/Postal code 84112
Country USA
 
Platform ID GPL6801
Series (1)
GSE29851 Genetic analysis of ancestry, admixture, and selection in Bolivian and Totonac populations of the New World

Data table header descriptions
ID_REF
VALUE Genotype call: 1=AA, 2=AC, 3=AG, 4=AT, 5=CA, 6=CC, 7=CG, 8=CT, 9=GA, 10=GG, 11=GT, 12=TC, 13=TG, and 14=TT

Data table
ID_REF VALUE
SNP_A-8709646 6
SNP_A-1909444 1
SNP_A-8408912 14
SNP_A-8524447 6
SNP_A-8573955 1
SNP_A-8573668 1
SNP_A-8573414 1
SNP_A-8531044 12
SNP_A-8530320
SNP_A-2116190 12
SNP_A-8325638 1
SNP_A-8700396 6
SNP_A-8411863 9
SNP_A-8420886 9
SNP_A-8513328 10
SNP_A-1902458 1
SNP_A-2131660 6
SNP_A-8450345 10
SNP_A-2109914 10
SNP_A-2291997 10

Total number of rows: 815376

Table truncated, full table size 13085 Kbytes.




Supplementary file Size Download File type/resource
GSM739549_TOT_F038958.CEL.gz 27.2 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap