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Sample GSM917649 Query DataSets for GSM917649
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-185 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 39.0
gender: F
histological subtype: Classic
subgroup: SHH
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-185
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 AB 0.002870 AB 1942.432251 1690.302734
SNP_A-1967418 BB 0.006069 BB 190.606018 678.242004
SNP_A-1969580 BB 0.005129 BB 1030.756958 4381.180176
SNP_A-4263484 BB 0.005843 BB 442.061340 1388.129883
SNP_A-1978185 AA 0.002831 AA 1046.877686 302.274261
SNP_A-4264431 AA 0.020015 AA 1509.037598 297.272003
SNP_A-1980898 BB 0.007481 BB 241.850967 1003.359985
SNP_A-1983139 AA 0.003126 AA 1485.824829 381.034210
SNP_A-4265735 AA 0.007796 AA 1161.764771 330.577698
SNP_A-1995832 AA 0.000732 AA 1952.761230 432.881134
SNP_A-1995893 AA 0.003801 AA 2382.496582 828.756958
SNP_A-1997689 BB 0.003996 BB 770.826294 3043.880859
SNP_A-1997709 AA 0.001758 AA 1790.498413 293.942993
SNP_A-1997896 AA 0.008712 AA 1567.761108 443.582367
SNP_A-1997922 AA 0.002930 AA 1143.082397 264.072937
SNP_A-2000230 AA 0.009230 AA 1905.471802 814.129089
SNP_A-2000332 AA 0.004425 AA 3594.023682 628.760864
SNP_A-2000337 AA 0.001734 AA 1500.295410 302.274261
SNP_A-2000342 AA 0.009946 AA 2749.331299 621.432800
SNP_A-4268172 AB 0.068647 AB 300.885986 865.252991

Total number of rows: 934968

Table truncated, full table size 47473 Kbytes.




Supplementary file Size Download File type/resource
GSM917649_MT377_MDT-MB-185.CEL.gz 28.8 Mb (ftp)(http) CEL
GSM917649_MT377_MDT-MB-185.birdseed.chp.gz 13.4 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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