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Sample GSM672455 Query DataSets for GSM672455
Status Public on Feb 17, 2011
Title 2377_Child (Mapping250_Sty)
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 GPL3720
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 0.010065 BB -0.828694 11.907067
AFFX-2315061 AB 0.015086 AB 0.241918 10.942167
AFFX-2315062 AA 0.018148 AA 0.570321 10.175497
AFFX-2315057 AA 0.019329 AA 0.462348 10.335739
AFFX-2315058 AA 0.023919 AA 0.807517 11.833238
AFFX-2315059 AA 0.005296 AA 0.850671 10.842009
AFFX-2315063 AA 0.000890 AA 0.790384 10.488186
AFFX-2315064 AA 0.015436 AA 0.736341 10.189447
AFFX-2315065 BB 0.047587 BB -0.431934 10.399896
AFFX-2315066 BB 0.002860 BB -0.710569 10.480430
AFFX-2315067 AA 0.023862 AA 0.709855 11.253500
AFFX-2315068 AB 0.037729 AB -0.039794 10.416177
AFFX-2315069 AB 0.017743 AB 0.003112 9.676948
AFFX-2315070 BB 0.046247 BB -0.609028 10.638728
AFFX-2315071 AB 0.016516 AB -0.189401 9.986696
AFFX-2315072 AB 0.006687 AB 0.134060 11.393170
AFFX-2315073 AB 0.048920 AB 0.286254 10.473928
AFFX-2315074 AB 0.013689 AB 0.136735 9.941720
AFFX-2315075 AA 0.015014 AA 0.795461 11.496678
AFFX-2315076 AB 0.018014 AB -0.094607 11.378934

Total number of rows: 238354

Table truncated, full table size 11206 Kbytes.

Supplementary file Size Download File type/resource
GSM672455_2377_Child_Sty.CEL.gz 25.3 Mb (ftp)(http) CEL
GSM672455_2377_Child_Sty.chp.gz 3.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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