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Sample GSM992930 Query DataSets for GSM992930
Status Public on Aug 28, 2012
Title PN11-0204
Sample type genomic
 
Source name peripheral (EDTA) blood
Organism Homo sapiens
Characteristics gender: female
Growth protocol No culture but direct isolation from peripheral blood
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isloated with a Chemagen/Hamilton magnetic bead DNA isolation robot
Label biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description Hybridized to 250K_Nsp
Data processing The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.0 and Copy Number Analyzer for Affymetrix GeneChip mapping (CNAGT 2.0) software. The inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAG2.0. Regions of homozygosity (LCSH/LOH) were determined with a likelihood based algorithm implemented in CNAG2.0.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
 
Submission date Aug 27, 2012
Last update date Aug 28, 2012
Contact name Rolph Pfundt
E-mail(s) Rolph.Pfundt@radboudumc.nl
Organization name RUNMC
Department Genetics
Lab Genome Diagnostics
Street address Geert Grooteplein Zuid 6
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
 
Platform ID GPL3718
Series (1)
GSE40405 CNV and LOH analysis of patient sample PN11-0204

Data table header descriptions
ID_REF
VALUE Genotypes: AA, AB, BB, No Call
CONFIDENCE
RAS1 Relative allele signal for the data in the first probe group
RAS2 Relative allele signal for the data in the second probe group
P-VALUE AA
P-VALUE AB
P-VALUE BB
P-VALUE NO CALL

Data table
ID_REF VALUE CONFIDENCE RAS1 RAS2 P-VALUE AA P-VALUE AB P-VALUE BB P-VALUE NO CALL
AFFX-5Q-123 No Call 0 0 0 0 0 0 0
AFFX-5Q-456 No Call 0 0 0 0 0 0 0
AFFX-5Q-789 No Call 0 0 0 0 0 0 0
AFFX-5Q-ABC No Call 0 0 0 0 0 0 0
AFFX-barcodeA No Call 0 0 0 0 0 0 0
AFFX-barcodeB No Call 0 0 0 0 0 0 0
AFFX-barcodeC No Call 0 0 0 0 0 0 0
AFFX-barcodeD No Call 0 0 0 0 0 0 0
AFFX-barcodeE No Call 0 0 0 0 0 0 0
AFFX-barcodeF No Call 0 0 0 0 0 0 0
AFFX-barcodeG No Call 0 0 0 0 0 0 0
AFFX-barcodeH No Call 0 0 0 0 0 0 0
AFFX-barcodeI No Call 0 0 0 0 0 0 0
AFFX-barcodeJ No Call 0 0 0 0 0 0 0
AFFX-barcodeK No Call 0 0 0 0 0 0 0
AFFX-barcodeL No Call 0 0 0 0 0 0 0
AFFX-barcodeM No Call 0 0 0 0 0 0 0
AFFX-barcodeN No Call 0 0 0 0 0 0 0
AFFX-barcodeO No Call 0 0 0 0 0 0 0
AFFX-barcodeP No Call 0 0 0 0 0 0 0

Total number of rows: 262338

Table truncated, full table size 20556 Kbytes.




Supplementary file Size Download File type/resource
GSM992930_PN11-0204.CEL.gz 28.3 Mb (ftp)(http) CEL
GSM992930_PN11-0204.CHP.gz 511.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file
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