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Sample GSM917647 Query DataSets for GSM917647
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-183 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 29.0
gender: M
histological subtype: Classic
subgroup: N/A
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-183
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 AA 0.005762 AA 1949.486206 582.443848
SNP_A-1967418 BB 0.016635 BB 276.958435 503.400391
SNP_A-1969580 BB 0.017033 BB 1281.323853 3365.716797
SNP_A-4263484 BB 0.009717 BB 511.896820 1326.713257
SNP_A-1978185 AA 0.001102 AA 1268.301880 292.862061
SNP_A-4264431 NC 0.680378 BB 441.071991 926.971191
SNP_A-1980898 NC 0.133041 BB 464.996735 993.219543
SNP_A-1983139 AA 0.006891 AA 1249.788330 302.003174
SNP_A-4265735 AB 0.027932 AB 1082.734497 632.382324
SNP_A-1995832 BB 0.081440 BB 1221.019165 2580.858643
SNP_A-1995893 BB 0.021792 BB 573.998291 1684.800049
SNP_A-1997689 BB 0.003384 BB 537.620728 2701.849854
SNP_A-1997709 AA 0.010806 AA 1089.532959 234.093964
SNP_A-1997896 AB 0.006172 AB 1758.053955 1960.423462
SNP_A-1997922 BB 0.034765 BB 378.971039 944.072021
SNP_A-2000230 AB 0.003256 AB 1617.800049 1818.081299
SNP_A-2000332 NC 0.164168 AA 3245.619873 1565.460327
SNP_A-2000337 AB 0.038275 AB 1333.101074 1032.241211
SNP_A-2000342 AA 0.022772 AA 2186.329590 742.702881
SNP_A-4268172 AA 0.021458 AA 333.699921 206.694550

Total number of rows: 934968

Table truncated, full table size 47484 Kbytes.




Supplementary file Size Download File type/resource
GSM917647_MT375_MDT-MB-183.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM917647_MT375_MDT-MB-183.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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