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Sample GSM917722 Query DataSets for GSM917722
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-317 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 4.0
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-317
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 0.007562 BB 684.648132 1959.403564
SNP_A-1967418 BB 0.005593 BB 250.397919 928.957214
SNP_A-1969580 BB 0.013997 BB 2217.307861 6113.994141
SNP_A-4263484 AB 0.035546 AB 1412.201782 1664.717896
SNP_A-1978185 AA 0.006512 AA 1413.207275 222.290619
SNP_A-4264431 AA 0.006841 AA 3204.324951 447.996277
SNP_A-1980898 AB 0.033247 AB 918.624451 1425.296143
SNP_A-1983139 AB 0.005504 AB 468.207886 676.583435
SNP_A-4265735 AA 0.001963 AA 1663.733521 478.393372
SNP_A-1995832 AB 0.038854 AB 1100.297485 1692.429199
SNP_A-1995893 AB 0.019318 AB 852.935425 1369.011841
SNP_A-1997689 BB 0.001276 BB 614.835876 2897.983398
SNP_A-1997709 AA 0.003428 AA 1459.397827 284.228210
SNP_A-1997896 NC 0.342278 AB 1374.018555 3180.589844
SNP_A-1997922 AA 0.003836 AA 1500.358521 294.793823
SNP_A-2000230 AA 0.003390 AA 2795.337891 952.696289
SNP_A-2000332 AB 0.031557 AB 2799.419678 1599.681641
SNP_A-2000337 AA 0.001366 AA 1580.752075 262.430817
SNP_A-2000342 AA 0.005718 AA 3233.519531 1034.960571
SNP_A-4268172 AA 0.024809 AA 1244.645386 310.414795

Total number of rows: 934968

Table truncated, full table size 47497 Kbytes.




Supplementary file Size Download File type/resource
GSM917722_MT18_MDT-MB-317.CEL.gz 29.5 Mb (ftp)(http) CEL
GSM917722_MT18_MDT-MB-317.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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