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Sample GSM917633 Query DataSets for GSM917633
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-166 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 1.0
gender: M
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-166
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 0.000773 AB 1546.436035 1631.100098
SNP_A-1967418 BB 0.002181 BB 236.588364 700.311340
SNP_A-1969580 BB 0.005006 BB 992.489929 3775.206055
SNP_A-4263484 AB 0.004807 AB 1352.339722 865.597961
SNP_A-1978185 AA 0.000960 AA 1179.259644 337.323212
SNP_A-4264431 AA 0.010527 AA 1798.675415 288.843964
SNP_A-1980898 AB 0.006504 AB 951.080322 608.392639
SNP_A-1983139 AA 0.005502 AA 1401.182251 330.916992
SNP_A-4265735 AB 0.006263 AB 732.880920 860.083679
SNP_A-1995832 BB 0.001412 BB 550.033569 1886.201172
SNP_A-1995893 BB 0.004242 BB 504.487061 2503.904297
SNP_A-1997689 BB 0.002366 BB 573.295105 2776.287109
SNP_A-1997709 AA 0.003130 AA 1451.938843 278.714569
SNP_A-1997896 AB 0.003078 AB 1334.405884 1901.827271
SNP_A-1997922 AB 0.003745 AB 844.487793 769.848389
SNP_A-2000230 AB 0.026307 AB 1034.870483 1288.211060
SNP_A-2000332 AB 0.002928 AB 2359.442871 2257.775146
SNP_A-2000337 AA 0.010907 AA 1102.654541 310.414154
SNP_A-2000342 AA 0.007958 AA 2755.351562 684.014099
SNP_A-4268172 AB 0.006890 AB 421.691864 662.814331

Total number of rows: 934968

Table truncated, full table size 47472 Kbytes.




Supplementary file Size Download File type/resource
GSM917633_MT359_MDT-MB-166.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM917633_MT359_MDT-MB-166.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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