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Sample GSM672840 Query DataSets for GSM672840
Status Public on Feb 17, 2011
Title 1780_Child (Mapping250K_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 1780
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 0.002142 BB -0.668613 12.229294
AFFX-2315061 AB 0.000973 AB 0.092949 11.295479
AFFX-2315062 AB 0.015404 AB -0.034107 10.959877
AFFX-2315057 AA 0.012663 AA 0.556894 10.927266
AFFX-2315058 BB 0.004103 BB -0.658219 10.975593
AFFX-2315059 AA 0.002174 AA 0.757853 10.667150
AFFX-2315063 AB 0.002203 AB -0.008464 11.124081
AFFX-2315064 AB 0.011827 AB 0.140627 11.127537
AFFX-2315065 BB 0.014505 BB -0.449862 10.668833
AFFX-2315066 BB 0.007818 BB -0.666047 10.798796
AFFX-2315067 AB 0.000748 AB 0.055679 11.222534
AFFX-2315068 AA 0.004803 AA 0.789364 10.932776
AFFX-2315069 AA 0.007864 AA 0.812693 10.746106
AFFX-2315070 AB 0.035369 AB -0.172420 11.081014
AFFX-2315071 AB 0.009388 AB -0.199657 9.845144
AFFX-2315072 AA 0.002480 AA 0.508099 10.968821
AFFX-2315073 AA 0.059040 AA 0.733481 11.178060
AFFX-2315074 AB 0.002544 AB 0.000969 10.603531
AFFX-2315075 AA 0.008185 AA 0.661406 11.824473
AFFX-2315076 AB 0.022709 AB -0.030306 11.053272

Total number of rows: 262314

Table truncated, full table size 12380 Kbytes.

Supplementary file Size Download File type/resource
GSM672840_1780_Child_Nsp.CEL.gz 26.3 Mb (ftp)(http) CEL
GSM672840_1780_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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