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Sample GSM672464 Query DataSets for GSM672464
Status Public on Feb 17, 2011
Title 4821_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: 4821
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 AA 0.006895 AA 0.562062 12.188769
AFFX-2315061 AA 0.001297 AA 0.839509 11.604038
AFFX-2315062 AA 0.017890 AA 0.579116 10.188621
AFFX-2315057 AB 0.069825 AB 0.038522 10.448833
AFFX-2315058 AA 0.068746 AA 0.634210 12.358231
AFFX-2315059 AB 0.003567 AB 0.205284 11.030285
AFFX-2315063 AA 0.014368 AA 0.801453 10.642785
AFFX-2315064 BB 0.045110 BB -0.433883 9.769098
AFFX-2315065 BB 0.016985 BB -0.401384 10.563286
AFFX-2315066 BB 0.019627 BB -0.674095 10.449574
AFFX-2315067 AB 0.012169 AB -0.086267 11.453743
AFFX-2315068 AB 0.007483 AB 0.197113 10.812078
AFFX-2315069 AB 0.012314 AB -0.127085 10.692062
AFFX-2315070 BB 0.020022 BB -0.568845 10.536536
AFFX-2315071 AB 0.005188 AB -0.203909 10.554566
AFFX-2315072 AA 0.097676 AA 0.542908 10.655051
AFFX-2315073 AA 0.011318 AA 0.670449 10.391166
AFFX-2315074 BB 0.164582 BB -0.278511 9.900928
AFFX-2315075 AB 0.016689 AB -0.024873 11.365458
AFFX-2315076 AB 0.019151 AB -0.072737 10.998178

Total number of rows: 238354

Table truncated, full table size 11260 Kbytes.

Supplementary file Size Download File type/resource
GSM672464_4821_Child_Sty.CEL.gz 26.4 Mb (ftp)(http) CEL
GSM672464_4821_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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