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Sample GSM672410 Query DataSets for GSM672410
Status Public on Feb 17, 2011
Title 2377_Child (Mapping250_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 2377
family member: Child
gender: Male
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from blood samples using the Puregene DNA kit
Label Biotin
Label protocol DNA samples were processed according to the instructions provided in the Affymetrix GeneChip® Mapping 500K Assay Manual
Hybridization protocol hybridized to GeneChip® Human Mapping 250K Nsp or 250K Sty arrays in an Affymetrix Hybridization Oven 640
Scan protocol images were obtained using an Affymetrix GeneChip® Scanner 3000 7G and GeneChip® Operating Software version 1.4
Data processing CNVs were detected using the Copy Number Analysis Tool (CNAT) (release cn-1.5.6_v3.2), which incorporates a Bayesian Robust Linear Model with the Mahalanobis distance classifier (BRLMM) algorithm to perform quantile normalization, followed by regression to reduce the PCR bias due to GC content and fragment length
An HMM-based algorithm implemented in CNAT4 was used to estimate copy number for each SNP in the context of its surrounding SNPs. The Gaussian bandwidth was set to 0 Kb and a minimum of 5 probes was required to detect a CNV. The findings were visualized using GeneChip Genotyping Analysis Software (GTYPE) from Affymetrix.
Submission date Feb 10, 2011
Last update date Feb 17, 2011
Contact name Tracy Tucker
Organization name University of British Columbia
Street address Box 153 4480 Oak Street
City Vancouver
ZIP/Postal code V6H3V4
Country Canada
Platform ID GPL3718
Series (2)
GSE27216 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (Mapping250K_Nsp and Mapping250K_Sty)
GSE27367 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR

Data table header descriptions

Data table
AFFX-2315060 BB 0.013848 BB -0.623258 11.896383
AFFX-2315061 AB 0.006224 AB 0.038794 11.058185
AFFX-2315062 AA 0.050627 AA 0.662925 10.397393
AFFX-2315057 AA 0.034497 AA 0.657835 10.685473
AFFX-2315058 AA 0.013028 AA 0.704465 11.354307
AFFX-2315059 AA 0.008560 AA 0.751759 10.401571
AFFX-2315063 AA 0.024837 AA 0.816678 10.800159
AFFX-2315064 AA 0.046354 AA 0.831158 11.008348
AFFX-2315065 BB 0.100980 BB -0.514452 10.608543
AFFX-2315066 BB 0.048590 BB -0.759624 10.564353
AFFX-2315067 AA 0.052894 AA 0.476486 11.150786
AFFX-2315068 AB 0.016992 AB 0.201020 10.842181
AFFX-2315069 AB 0.006258 AB -0.116023 10.738444
AFFX-2315070 BB 0.068992 BB -0.789437 10.749711
AFFX-2315071 AB 0.036221 AB 0.006902 9.876641
AFFX-2315072 AB 0.003689 AB -0.087869 10.741505
AFFX-2315073 AB 0.023642 AB 0.106302 10.881855
AFFX-2315074 AB 0.025833 AB -0.063408 10.405044
AFFX-2315075 AA 0.021468 AA 0.707046 11.574459
AFFX-2315076 AB 0.073184 AB 0.142251 10.755419

Total number of rows: 262314

Table truncated, full table size 12369 Kbytes.

Supplementary file Size Download File type/resource
GSM672410_2377_Child_Nsp.CEL.gz 25.7 Mb (ftp)(http) CEL
GSM672410_2377_Child_Nsp.chp.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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