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Sample GSM639794 Query DataSets for GSM639794
Status Public on Apr 07, 2011
Title Patient derived melanoma metastasis
Sample type genomic
 
Source name melanoma metastasis
Organism Homo sapiens
Characteristics gender: female
age: 58y
tissue: axilla melanoma metastasis
Extracted molecule genomic DNA
Extraction protocol DNA was isolated by using the All Prep DNA Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
Label biotin
Label protocol According to manufacturer protocol Affymetrix dsDNA terminal label
 
Hybridization protocol According to manufacturer protocol
Scan protocol According to manufacturer protocol
Data processing CEL files were processed via the genotyping console 3.0.1 using default parameters. CHP files were generated via the genotyping console 3.0.1 using default parameters. Normalization was performed using the birdseed v2 algorithm.
 
Submission date Dec 14, 2010
Last update date Apr 07, 2011
Contact name Mario Mikula
Organization name Medical University Vienna
Department General Dermatology
Lab SERD
Street address WaehringergĂĽrtel 18-20
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platform ID GPL6801
Series (1)
GSE26053 Tissue samples from the same individual patient

Data table header descriptions
ID_REF PROBE SET NAME
VALUE Genotype Call (SNP call): AA, AB, BB, NC, and NoCall
CONFIDENCE A value in the range [0,1] with lower values corresponding to greater confidence
FORCED CALL This value is the genotyping call that would be made if the calling algorithm were tuned to the least stringency. Providing this value allows for determining what the calls would have been at a stringency different to that applied to the calls in the second field, without having to re-run the genotyping algorithm
SIGNAL A Summarized signal A
SIGNAL B Summarized signal B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 AB 0.003480 AB 2609.075439 1776.400391
SNP_A-1967418 AA 0.003144 AA 881.207703 202.250656
SNP_A-1969580 BB 0.002447 BB 897.155273 3338.397217
SNP_A-4263484 NC 0.189427 AB 1613.924927 356.732056
SNP_A-1978185 AA 0.008466 AA 1356.808594 468.211578
SNP_A-4264431 AA 0.001245 AA 1961.870605 322.671570
SNP_A-1980898 BB 0.008987 BB 328.389618 828.808350
SNP_A-1983139 AA 0.003084 AA 665.367615 329.724060
SNP_A-4265735 AB 0.008614 AB 1081.403076 829.119263
SNP_A-1995832 NC 0.196574 AA 1435.746460 313.654816
SNP_A-1995893 AA 0.001406 AA 2115.188477 893.615784
SNP_A-1997689 BB 0.004010 BB 698.328125 2566.998047
SNP_A-1997709 AA 0.001490 AA 1504.736572 231.151260
SNP_A-1997896 AA 0.002955 AA 1140.680176 476.255920
SNP_A-1997922 AA 0.001150 AA 838.666260 305.900269
SNP_A-2000230 AA 0.001816 AA 2597.721680 1258.347656
SNP_A-2000332 AB 0.004013 AB 2520.340332 2264.652100
SNP_A-2000337 AA 0.001707 AA 1920.224731 247.998474
SNP_A-2000342 AA 0.005756 AA 3523.715088 871.864197
SNP_A-4268173 NC 0.189498 BB 226.467392 1806.795044

Total number of rows: 909622

Table truncated, full table size 46146 Kbytes.




Supplementary file Size Download File type/resource
GSM639794.CEL.gz 29.8 Mb (ftp)(http) CEL
GSM639794.chp.gz 13.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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