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Sample GSM917616 Query DataSets for GSM917616
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-145 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 10.0
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-145
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 0.002135 BB 623.202881 2189.989258
SNP_A-1967418 AB 0.003999 AB 509.082001 503.063293
SNP_A-1969580 BB 0.003119 BB 1091.449463 4066.043701
SNP_A-4263484 AA 0.015932 AA 1739.055054 360.015472
SNP_A-1978185 AA 0.002367 AA 1068.713623 281.524780
SNP_A-4264431 AA 0.005532 AA 3098.121582 405.037933
SNP_A-1980898 AB 0.001248 AB 998.359802 820.682068
SNP_A-1983139 AA 0.003581 AA 1358.315918 368.692627
SNP_A-4265735 AA 0.004236 AA 1347.370483 389.517090
SNP_A-1995832 BB 0.007235 BB 523.513123 1323.420044
SNP_A-1995893 BB 0.003393 BB 443.576508 1955.917847
SNP_A-1997689 BB 0.001774 BB 654.901611 2869.208496
SNP_A-1997709 AA 0.011009 AA 1146.151733 275.331879
SNP_A-1997896 AB 0.001408 AB 1473.047119 1995.936890
SNP_A-1997922 AB 0.003212 AB 806.064270 894.893799
SNP_A-2000230 AA 0.003174 AA 2736.599365 929.113098
SNP_A-2000332 AB 0.002174 AB 2286.795166 2410.609375
SNP_A-2000337 AA 0.001370 AA 1706.491455 285.969299
SNP_A-2000342 AA 0.004749 AA 3870.081299 965.676392
SNP_A-4268172 AA 0.003178 AA 626.014465 253.064178

Total number of rows: 934968

Table truncated, full table size 47486 Kbytes.




Supplementary file Size Download File type/resource
GSM917616_MT331_MDT-MB-145.CEL.gz 29.9 Mb (ftp)(http) CEL
GSM917616_MT331_MDT-MB-145.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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