NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM163447 Query DataSets for GSM163447
Status Public on Feb 20, 2007
Title 671
Sample type genomic
 
Source name blood or lymphoblast
Organism Homo sapiens
Characteristics familyID=2035-3;gender=M;status=affected;relation=siblings
Extracted molecule genomic DNA
Extraction protocol standard phenol/chloroform method
Label Biotin Streptavidin Phycoerythin (SAPE)
Label protocol See Affymetrix GeneChip Mapping 10K 2.0 Assay Manual, experiments were run in 96-well plate format 1. Prepare Labeling Mix as master mix ON ICE and vortex at medium speed for 2 seconds (for multiple samples, make 5% excess). 2. Aliquot 19.4 uL of Labeling Master Mix into the fragmentation plate containing 50.6 uL of fragmented DNA samples. 3. Seal the plate tightly with a plate cover. 4. Vortex the plate at medium speed for 2 seconds, and briefly spin the plate at 2,000 rpm for 1 minute. 5. Run the following program: 37ºC for 2 hours, 95ºC for 15 minutes, 4ºC Hold. 6. Briefly spin the plate at 2,000 rpm for 1 minute after the labeling reaction.
 
Hybridization protocol See Affymetrix GeneChip Mapping 10K 2.0 Assay. 1. Prepare the Hybridization Cocktail Master Mix (for multiple samples make 5% excess). 2. Transfer each of the labeled sample from the plate to a 1.5 mL Eppendorf tube. Aliquot 190 uL of the Hybridization Cocktail Master Mix into the 70 uL of labeled DNA samples. 3. Heat the 260 uL of hybridization mix and labeled DNA at 95°C in a heat block for 10 minutes to denature. 4. Cool down on crushed ice for 10 seconds. 5. Spin briefly at 2,000 rpm for 1 minute in a microfuge to collect any condensate. 6. Place the tubes at 48°C for 2 minutes. 7. Inject 80 uL denatured hybridization mix into the array. 8. Hybridize at 48°C for 16 to 18 hours at 60 rpm.
Scan protocol See Affymetrix GeneChip Mapping 10K 2.0 Assay Manual. Fluidics Station 450/250 was used to automate the washing and staining of GeneChip® Mapping probe arrays. Arrays were scanned with the GeneChip® Scanner 3000 using GeneChip Operating Software (GCOS)
Description NAAR048-E2-02C09752
Data processing Genotype calls were made using Affymetrix GeneChip Operating Software (GCOS) and Affymetrix GeneChip DNA Analysis Software (GDAS). Copy number variation was inferred using DNA Chip Analyzer (dCHIP).
 
Submission date Feb 18, 2007
Last update date Feb 21, 2007
Contact name Christian R. Marshall
URL http://www.tcag.ca/
Organization name The Hospital for Sick Children
Department Genetics & Genome Biology
Street address 101 College St.
City Toronto
State/province ON
ZIP/Postal code M5G 1L7
Country Canada
 
Platform ID GPL2641
Series (1)
GSE6754 Mapping autism risk loci using genetic linkage and chromosomal rearrangements

Data table header descriptions
ID_REF
VALUE Genotypes: AA, AB, BB, No Call
CONFIDENCE
RAS1 Relative allele signal for the data in the first probe group
RAS2 Relative allele signal for the data in the second probe group
P-VALUE AA
P-VALUE AB
P-VALUE BB
P-VALUE NO CALL

Data table
ID_REF VALUE CONFIDENCE RAS1 RAS2 P-VALUE AA P-VALUE AB P-VALUE BB P-VALUE NO CALL
AFFX-5Q-123 No Call 12234.5 0 0 0 0 0 0
AFFX-5Q-456 No Call 3453 0 0 0 0 0 0
AFFX-5Q-789 No Call 15667 0 0 0 0 0 0
AFFX-5Q-ABC No Call 16828.5 0 0 0 0 0 0
SNP_A-1513509 BB 0.0285218 0.0452323 0 0.0452323 0 0 0
SNP_A-1518411 BB 0.104432 0.0402711 0.0482063 0.0402711 0.0482063 0 0
SNP_A-1511066 AA 0.276281 0.934709 0.888073 0.934709 0.888073 0 0
SNP_A-1517367 AA 0.170085 0.969699 1 0.969699 1 0 0
SNP_A-1512567 No Call 0.872017 0.435991 0.756485 0.435991 0.756485 0 0
SNP_A-1519604 AB 0.19225 0.198148 0.489189 0.198148 0.489189 0 0
SNP_A-1507932 AB 0.543532 0.354962 0.37099 0.354962 0.37099 0 0
SNP_A-1519685 AB 0.556897 0.557621 0.421733 0.557621 0.421733 0 0
SNP_A-1516165 AB 0.234386 0.771016 0.641869 0.771016 0.641869 0 0
SNP_A-1514890 AB 0.371359 0.308136 0.436441 0.308136 0.436441 0 0
SNP_A-1507580 BB 0.244118 0.0483676 0 0.0483676 0 0 0
SNP_A-1510991 AA 0.037608 0.993323 0.942441 0.993323 0.942441 0 0
SNP_A-1516205 AA 0.0827894 1 0.926154 1 0.926154 0 0
SNP_A-1512666 BB 0 0 0 0 0 0 0
SNP_A-1512740 BB 0.329162 0.0431499 0.0410163 0.0431499 0.0410163 0 0
SNP_A-1512132 AA 0.481842 0.843804 0.911009 0.843804 0.911009 0 0

Total number of rows: 10208

Table truncated, full table size 589 Kbytes.




Supplementary file Size Download File type/resource
GSM163447.CEL.gz 1.9 Mb (ftp)(http) CEL
GSM163447.CHP.gz 108.1 Kb (ftp)(http) CHP
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.