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Sample GSM917303 Query DataSets for GSM917303
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-8 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 11.1
gender: M
histological subtype: Large Cell/Anaplastic
subgroup: Group 3
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-8
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 0.001870 BB 498.496613 2174.322998
SNP_A-1967418 BB 0.019770 BB 285.643860 1148.064575
SNP_A-1969580 BB 0.025717 BB 2487.072998 6233.705566
SNP_A-4263484 BB 0.000338 BB 520.621704 1762.721802
SNP_A-1978185 AA 0.005139 AA 1373.871948 230.425064
SNP_A-4264431 AA 0.007061 AA 3174.535645 512.016357
SNP_A-1980898 BB 0.017060 BB 428.023529 2216.577881
SNP_A-1983139 AA 0.008221 AA 1869.987061 664.393005
SNP_A-4265735 AB 0.006442 AB 1425.808472 1194.072388
SNP_A-1995832 BB 0.037634 BB 649.242432 2811.943848
SNP_A-1995893 BB 0.002690 BB 462.000977 2023.817993
SNP_A-1997689 BB 0.007225 BB 560.586548 2315.680420
SNP_A-1997709 AA 0.010503 AA 1141.100830 268.828857
SNP_A-1997896 AB 0.003097 AB 1717.879028 2286.351807
SNP_A-1997922 AB 0.007943 AB 790.195679 672.997253
SNP_A-2000230 AA 0.011681 AA 2069.932129 654.438538
SNP_A-2000332 AA 0.003504 AA 3764.368896 950.770691
SNP_A-2000337 AA 0.006469 AA 1714.110352 220.460236
SNP_A-2000342 AA 0.008088 AA 2839.406982 941.693970
SNP_A-4268172 AA 0.000847 AA 724.115234 269.944580

Total number of rows: 934968

Table truncated, full table size 47507 Kbytes.




Supplementary file Size Download File type/resource
GSM917303_MT635_MDT-MB-8.CEL.gz 29.6 Mb (ftp)(http) CEL
GSM917303_MT635_MDT-MB-8.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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