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Sample GSM917699 Query DataSets for GSM917699
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-221 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 9.6
gender: F
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-221
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 0.003747 BB 551.953491 1973.737427
SNP_A-1967418 BB 0.009020 BB 347.379242 990.660156
SNP_A-1969580 BB 0.005261 BB 1789.608765 5617.097168
SNP_A-4263484 AB 0.001792 AB 1807.573608 1274.513916
SNP_A-1978185 AA 0.007204 AA 878.269775 293.295227
SNP_A-4264431 AA 0.011860 AA 3324.176270 374.497986
SNP_A-1980898 AB 0.011752 AB 1516.012451 1188.886353
SNP_A-1983139 AA 0.002891 AA 1623.930908 403.143188
SNP_A-4265735 AB 0.004183 AB 873.026672 836.240051
SNP_A-1995832 BB 0.001665 BB 524.915710 1887.335449
SNP_A-1995893 BB 0.003726 BB 546.047852 2214.107666
SNP_A-1997689 BB 0.002903 BB 718.933655 2926.642578
SNP_A-1997709 AA 0.004725 AA 1320.439941 254.368546
SNP_A-1997896 AB 0.003909 AB 1759.833740 2296.239990
SNP_A-1997922 AB 0.001720 AB 950.715027 994.463562
SNP_A-2000230 AA 0.002643 AA 2345.177002 1069.067017
SNP_A-2000332 AA 0.004701 AA 3652.125244 1050.435913
SNP_A-2000337 AA 0.005399 AA 1255.963623 279.291168
SNP_A-2000342 AA 0.001272 AA 3554.146729 909.304993
SNP_A-4268172 AA 0.006860 AA 940.740295 229.576736

Total number of rows: 934968

Table truncated, full table size 47483 Kbytes.




Supplementary file Size Download File type/resource
GSM917699_MT411_MDT-MB-221.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM917699_MT411_MDT-MB-221.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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