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Sample GSM917710 Query DataSets for GSM917710
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-303 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 13.0
gender: M
histological subtype: Classic
subgroup: WNT
Treatment protocol N/A
Growth protocol N/A
Extracted molecule genomic DNA
Extraction protocol High molecular weight genomic DNA was extracted from primary tissue and cell lines using either the standard SDS/Proteinase K method or Qiagen DNEasy Blood and Tissue Kits.
Label Biotin
Label protocol As directed by the manufacturer (Affymetrix)
 
Hybridization protocol As directed by the manufacturer (Affymetrix)
Scan protocol As directed by the manufacturer (Affymetrix)
Description MDT-MB-303
Data processing SNP genotyping was performed using the birdseed algorithm (v2) available in Affymetrix Genotyping Console 4.0. For copy number analysis, CEL files were quantile normalized and signal intensities estimated using the MBEI method in dChip.
 
Submission date Apr 18, 2012
Last update date Jul 27, 2012
Contact name Paul A. Northcott
E-mail(s) panorthcott@gmail.com
Organization name German Cancer Research Center (DKFZ)
Street address Im Neuenheimer Feld 280
City HEIDELBERG
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL6801
Series (2)
GSE37384 Subgroup specific somatic copy number aberrations in the medulloblastoma genome [gDNA]
GSE37385 Subgroup specific somatic copy number aberrations in the medulloblastoma genome

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 BB 0.013330 BB 675.297852 1832.966919
SNP_A-1967418 AB 0.002147 AB 568.256592 476.560547
SNP_A-1969580 BB 0.007007 BB 1937.112427 5718.184082
SNP_A-4263484 AB 0.002816 AB 1934.884644 1280.828491
SNP_A-1978185 AA 0.002759 AA 1073.694458 243.302917
SNP_A-4264431 AB 0.012330 AB 2195.262695 1686.195068
SNP_A-1980898 BB 0.003084 BB 352.885376 1728.328003
SNP_A-1983139 AA 0.012198 AA 993.071838 232.520142
SNP_A-4265735 AA 0.001762 AA 1670.430786 474.311279
SNP_A-1995832 AB 0.002704 AB 1248.724731 1206.150513
SNP_A-1995893 AB 0.004071 AB 1320.943359 1342.723877
SNP_A-1997689 BB 0.002886 BB 598.471313 2690.309570
SNP_A-1997709 AA 0.002862 AA 1899.954956 284.654236
SNP_A-1997896 AA 0.006242 AA 2602.320557 583.243469
SNP_A-1997922 AB 0.005984 AB 1155.590942 1023.880859
SNP_A-2000230 AA 0.009082 AA 3044.244141 909.494995
SNP_A-2000332 AA 0.003798 AA 3800.046387 788.772766
SNP_A-2000337 AA 0.000375 AA 1572.295166 277.496429
SNP_A-2000342 AA 0.001563 AA 3189.455811 872.791748
SNP_A-4268172 AA 0.007568 AA 1011.282776 279.792633

Total number of rows: 934968

Table truncated, full table size 47494 Kbytes.




Supplementary file Size Download File type/resource
GSM917710_MT4_MDT-MB-303.CEL.gz 29.1 Mb (ftp)(http) CEL
GSM917710_MT4_MDT-MB-303.birdseed.chp.gz 13.5 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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