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Sample GSM672846 Query DataSets for GSM672846
Status Public on Feb 17, 2011
Title 2714_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: 2714
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
E-mail(s) tbtucker@interchange.ubc.ca
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
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
CONTRAST
STRENGTH

Data table
ID_REF VALUE CONFIDENCE FORCED CALL CONTRAST STRENGTH
AFFX-2315060 BB 0.004595 BB -0.632301 12.163367
AFFX-2315061 AB 0.004497 AB 0.171852 11.258940
AFFX-2315062 AA 0.003013 AA 0.602427 10.664974
AFFX-2315057 BB 0.025017 BB -0.562840 11.009522
AFFX-2315058 AA 0.008822 AA 0.666450 11.502059
AFFX-2315059 AB 0.000166 AB 0.232830 10.592957
AFFX-2315063 AB 0.006281 AB -0.030629 10.897991
AFFX-2315064 BB 0.000524 BB -0.699674 10.754591
AFFX-2315065 BB 0.132742 BB -0.381400 10.622840
AFFX-2315066 AB 0.001318 AB 0.048913 10.741978
AFFX-2315067 BB 0.009090 BB -0.516021 11.107477
AFFX-2315068 BB 0.001659 BB -0.664489 10.870021
AFFX-2315069 AB 0.002504 AB -0.162729 10.825516
AFFX-2315070 BB 0.055253 BB -0.595514 10.978793
AFFX-2315071 BB 0.005724 BB -0.695101 9.890105
AFFX-2315072 AA 0.005275 AA 0.550178 10.923612
AFFX-2315073 AB 0.010058 AB 0.236474 10.834570
AFFX-2315074 BB 0.035344 BB -0.532836 10.504579
AFFX-2315075 AA 0.009046 AA 0.662475 11.746643
AFFX-2315076 BB 0.010149 BB -0.509094 11.007309

Total number of rows: 262314

Table truncated, full table size 12378 Kbytes.




Supplementary file Size Download File type/resource
GSM672846_2714_Child_Nsp.CEL.gz 26.4 Mb (ftp)(http) CEL
GSM672846_2714_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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