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Sample GSM917435 Query DataSets for GSM917435
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-130 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 11.0
gender: M
histological subtype: Classic
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-130
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 0.000841 AB 1754.518799 1700.316284
SNP_A-1967418 BB 0.000146 BB 271.703491 778.937500
SNP_A-1969580 BB 0.001003 BB 1274.761353 4472.666504
SNP_A-4263484 AA 0.004541 AA 2090.048096 347.426147
SNP_A-1978185 AA 0.002374 AA 1092.914062 251.874344
SNP_A-4264431 AB 0.000977 AB 1749.274170 1271.197998
SNP_A-1980898 BB 0.002478 BB 227.179199 1339.056396
SNP_A-1983139 AA 0.003667 AA 1431.391846 502.350220
SNP_A-4265735 AA 0.002002 AA 1835.262817 477.609924
SNP_A-1995832 BB 0.001307 BB 549.122375 1877.470459
SNP_A-1995893 BB 0.004111 BB 519.671448 2489.621338
SNP_A-1997689 BB 0.001515 BB 706.165588 3331.889648
SNP_A-1997709 AA 0.002172 AA 1523.396240 281.663269
SNP_A-1997896 AB 0.001174 AB 1600.367798 2206.793457
SNP_A-1997922 AB 0.005649 AB 1153.546021 972.309509
SNP_A-2000230 AA 0.002000 AA 2323.965820 961.910461
SNP_A-2000332 AA 0.006757 AA 4008.211426 821.006470
SNP_A-2000337 AA 0.004142 AA 1334.630859 301.967346
SNP_A-2000342 AA 0.002306 AA 3495.421631 979.488403
SNP_A-4268172 AB 0.001848 AB 508.822601 864.881653

Total number of rows: 934968

Table truncated, full table size 47482 Kbytes.




Supplementary file Size Download File type/resource
GSM917435_MT317_MDT-MB-130.CEL.gz 30.1 Mb (ftp)(http) CEL
GSM917435_MT317_MDT-MB-130.birdseed.chp.gz 13.6 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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