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Sample GSM917390 Query DataSets for GSM917390
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-108 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 0.9
gender: F
histological subtype: Desmoplastic
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-108
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 0.000684 AB 1629.830933 1551.303223
SNP_A-1967418 BB 0.004177 BB 306.232758 919.872253
SNP_A-1969580 BB 0.008000 BB 1400.619751 5412.721680
SNP_A-4263484 BB 0.000640 BB 476.272064 1730.291016
SNP_A-1978185 AA 0.002813 AA 1126.978149 226.511612
SNP_A-4264431 AA 0.010012 AA 3247.353760 369.470825
SNP_A-1980898 AB 0.005207 AB 1280.143188 845.070068
SNP_A-1983139 AA 0.002468 AA 1381.637451 437.748047
SNP_A-4265735 AB 0.000743 AB 1024.569580 1069.037964
SNP_A-1995832 BB 0.001625 BB 458.039368 1693.150635
SNP_A-1995893 BB 0.001362 BB 448.873230 2312.357910
SNP_A-1997689 BB 0.003394 BB 736.293945 3575.857422
SNP_A-1997709 AA 0.006327 AA 1315.166504 221.159378
SNP_A-1997896 AB 0.000457 AB 1518.690186 2201.951172
SNP_A-1997922 AB 0.004220 AB 1003.749573 1080.071533
SNP_A-2000230 AA 0.010387 AA 3049.458984 878.021057
SNP_A-2000332 AA 0.002105 AA 3239.325684 690.507996
SNP_A-2000337 AA 0.000995 AA 1653.321411 272.234497
SNP_A-2000342 AA 0.005529 AA 3927.484863 956.424683
SNP_A-4268172 BB 0.014384 BB 234.423462 1801.118286

Total number of rows: 934968

Table truncated, full table size 47489 Kbytes.




Supplementary file Size Download File type/resource
GSM917390_MT289_MDT-MB-108.CEL.gz 28.3 Mb (ftp)(http) CEL
GSM917390_MT289_MDT-MB-108.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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