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Sample GSM917331 Query DataSets for GSM917331
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-42 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 7.0
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-42
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 0.048039 AB 1492.396484 879.455688
SNP_A-1967418 AB 0.008257 AB 439.936951 435.480255
SNP_A-1969580 BB 0.005606 BB 1743.537231 4834.778320
SNP_A-4263484 BB 0.015025 BB 376.761871 1088.801880
SNP_A-1978185 AA 0.002651 AA 1052.494263 280.651581
SNP_A-4264431 AA 0.004198 AA 2152.912842 307.283539
SNP_A-1980898 AB 0.005766 AB 924.576050 1043.778320
SNP_A-1983139 AA 0.003374 AA 1312.761475 385.480743
SNP_A-4265735 BB 0.012177 BB 283.682465 1061.341187
SNP_A-1995832 AB 0.021167 AB 1181.170776 1602.626953
SNP_A-1995893 AB 0.032257 AB 738.040588 1458.880249
SNP_A-1997689 BB 0.009407 BB 649.340759 2278.758789
SNP_A-1997709 AA 0.010197 AA 1142.079590 215.117447
SNP_A-1997896 AB 0.019248 AB 1307.923828 2774.530518
SNP_A-1997922 AA 0.008890 AA 990.779053 298.018341
SNP_A-2000230 AA 0.013037 AA 1740.524292 862.308411
SNP_A-2000332 AB 0.006273 AB 2046.607300 2561.754883
SNP_A-2000337 AA 0.003954 AA 1370.830566 254.495911
SNP_A-2000342 AA 0.006118 AA 2877.685547 899.288513
SNP_A-4268172 AA 0.003340 AA 623.162903 233.062836

Total number of rows: 934968

Table truncated, full table size 47499 Kbytes.




Supplementary file Size Download File type/resource
GSM917331_MT665_MDT-MB-42.CEL.gz 29.3 Mb (ftp)(http) CEL
GSM917331_MT665_MDT-MB-42.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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