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Sample GSM917679 Query DataSets for GSM917679
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-198 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 5.0
gender: F
histological subtype: Classic
subgroup: SHH
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-198
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 0.015612 AB 2443.753662 2435.776367
SNP_A-1967418 AB 0.006739 AB 459.600891 468.116943
SNP_A-1969580 BB 0.002450 BB 1152.999634 4378.017090
SNP_A-4263484 AB 0.003391 AB 1853.992676 1085.099731
SNP_A-1978185 AA 0.012622 AA 1757.070557 438.428009
SNP_A-4264431 AA 0.011104 AA 1808.517700 334.775818
SNP_A-1980898 BB 0.006026 BB 314.336426 1125.494751
SNP_A-1983139 AA 0.000390 AA 1616.970215 475.260681
SNP_A-4265735 AB 0.003316 AB 853.921082 965.868958
SNP_A-1995832 BB 0.001194 BB 523.796692 1850.526245
SNP_A-1995893 BB 0.012104 BB 414.791626 2702.942139
SNP_A-1997689 BB 0.006846 BB 759.382263 3884.747559
SNP_A-1997709 AA 0.005110 AA 1830.728516 241.307831
SNP_A-1997896 BB 0.007854 BB 630.601440 2671.317871
SNP_A-1997922 AA 0.001161 AA 1231.397461 269.724701
SNP_A-2000230 AA 0.017308 AA 1883.989868 1152.426636
SNP_A-2000332 AB 0.005542 AB 2064.501953 2338.258545
SNP_A-2000337 AA 0.002162 AA 1437.689697 296.033295
SNP_A-2000342 AA 0.006477 AA 3130.186035 1024.074219
SNP_A-4268172 AA 0.004454 AA 586.366943 229.238480

Total number of rows: 934968

Table truncated, full table size 47476 Kbytes.




Supplementary file Size Download File type/resource
GSM917679_MT390_MDT-MB-198.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM917679_MT390_MDT-MB-198.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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