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Sample GSM672412 Query DataSets for GSM672412
Status Public on Feb 17, 2011
Title 2377_Child_Mother (Mapping250_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2377
family member: Mother
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 AB 0.011481 AB -0.053534 11.994760
AFFX-2315061 AB 0.003502 AB 0.139522 11.035232
AFFX-2315062 AA 0.001845 AA 0.531892 10.362397
AFFX-2315057 AA 0.002683 AA 0.499439 10.523541
AFFX-2315058 AA 0.001885 AA 0.714749 11.239081
AFFX-2315059 AA 0.010029 AA 0.764752 10.552974
AFFX-2315063 AA 0.007906 AA 0.754803 10.654277
AFFX-2315064 AB 0.023147 AB 0.297395 10.929196
AFFX-2315065 BB 0.012427 BB -0.501757 10.396535
AFFX-2315066 BB 0.023052 BB -0.721105 10.489157
AFFX-2315067 AA 0.047931 AA 0.479303 11.146456
AFFX-2315068 AB 0.014357 AB 0.094155 10.792324
AFFX-2315069 AB 0.009890 AB -0.052476 10.705666
AFFX-2315070 BB 0.006663 BB -0.639912 10.690221
AFFX-2315071 AB 0.005712 AB -0.170776 9.898677
AFFX-2315072 AB 0.008236 AB -0.083990 10.832878
AFFX-2315073 BB 0.013385 BB -0.654725 10.640470
AFFX-2315074 AB 0.005398 AB 0.061753 10.403521
AFFX-2315075 AB 0.002399 AB 0.112651 11.501871
AFFX-2315076 AB 0.040838 AB 0.054092 10.864433

Total number of rows: 262314

Table truncated, full table size 12369 Kbytes.

Supplementary file Size Download File type/resource
GSM672412_2377_Mother_Nsp.CEL.gz 25.9 Mb (ftp)(http) CEL
GSM672412_2377_Mother_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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