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Sample GSM917641 Query DataSets for GSM917641
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-177 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 10.0
gender: M
histological subtype: Large Cell/Anaplastic
subgroup: Group 4
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-177
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 0.001364 AB 1815.772827 1713.179810
SNP_A-1967418 BB 0.002856 BB 229.914825 680.304810
SNP_A-1969580 BB 0.010167 BB 1280.471558 5311.855957
SNP_A-4263484 BB 0.006918 BB 305.485870 1319.484497
SNP_A-1978185 AA 0.002446 AA 1064.011353 292.368225
SNP_A-4264431 AA 0.018314 AA 1570.191040 316.961975
SNP_A-1980898 BB 0.006961 BB 247.545166 1024.887939
SNP_A-1983139 AA 0.003793 AA 1286.283447 374.374207
SNP_A-4265735 AA 0.049329 AA 1058.943726 442.407867
SNP_A-1995832 NC 0.549395 AA 1476.806030 588.959290
SNP_A-1995893 AA 0.002254 AA 2302.374756 844.511414
SNP_A-1997689 BB 0.000761 BB 682.024414 3222.940674
SNP_A-1997709 AA 0.000909 AA 1591.761230 276.106140
SNP_A-1997896 AA 0.005237 AA 1736.115234 477.076630
SNP_A-1997922 AA 0.004471 AA 1086.431763 244.011047
SNP_A-2000230 AA 0.012800 AA 1806.234131 1004.602417
SNP_A-2000332 AB 0.007716 AB 2256.866943 1979.996948
SNP_A-2000337 AA 0.000899 AA 1659.271729 290.728058
SNP_A-2000342 AA 0.005239 AA 2863.069824 765.635681
SNP_A-4268172 AB 0.009988 AB 422.784943 583.158630

Total number of rows: 934968

Table truncated, full table size 47476 Kbytes.




Supplementary file Size Download File type/resource
GSM917641_MT369_MDT-MB-177.CEL.gz 28.7 Mb (ftp)(http) CEL
GSM917641_MT369_MDT-MB-177.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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