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Sample GSM917645 Query DataSets for GSM917645
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-181 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 4.0
gender: F
histological subtype: Classic
subgroup: Group 3
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-181
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 0.022635 BB 707.876953 1801.614624
SNP_A-1967418 BB 0.005627 BB 248.267044 586.150085
SNP_A-1969580 BB 0.003172 BB 1096.934448 4035.740723
SNP_A-4263484 AA 0.012877 AA 1727.072021 294.958496
SNP_A-1978185 AA 0.002096 AA 1085.098999 282.916901
SNP_A-4264431 AA 0.028714 AA 1347.766724 310.629059
SNP_A-1980898 NC 0.110658 AA 1073.723633 274.542267
SNP_A-1983139 AA 0.004369 AA 1218.980713 385.351166
SNP_A-4265735 NC 0.303004 AA 944.650269 441.126099
SNP_A-1995832 AA 0.003292 AA 1774.079346 408.153839
SNP_A-1995893 AA 0.006043 AA 1898.556274 925.726135
SNP_A-1997689 BB 0.008581 BB 724.239685 2484.232666
SNP_A-1997709 AA 0.000898 AA 1670.925415 285.308228
SNP_A-1997896 AA 0.016616 AA 1314.438110 380.351532
SNP_A-1997922 AA 0.013187 AA 884.208740 253.055908
SNP_A-2000230 AA 0.023944 AA 1488.758057 887.614380
SNP_A-2000332 BB 0.006754 BB 1123.892334 3081.781982
SNP_A-2000337 AA 0.013701 AA 1134.285767 217.496414
SNP_A-2000342 AA 0.017317 AA 2351.452637 646.446777
SNP_A-4268172 AA 0.009642 AA 475.498657 238.205322

Total number of rows: 934968

Table truncated, full table size 47477 Kbytes.




Supplementary file Size Download File type/resource
GSM917645_MT373_MDT-MB-181.CEL.gz 29.0 Mb (ftp)(http) CEL
GSM917645_MT373_MDT-MB-181.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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