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Sample GSM917340 Query DataSets for GSM917340
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-53 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 2.0
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-53
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 0.005376 BB 559.842041 2967.381836
SNP_A-1967418 BB 0.009610 BB 252.364471 526.072815
SNP_A-1969580 BB 0.008850 BB 1829.562988 5964.519531
SNP_A-4263484 AA 0.014438 AA 3177.856934 399.330902
SNP_A-1978185 AA 0.008656 AA 1592.095703 299.472839
SNP_A-4264431 AA 0.003535 AA 2203.669678 343.606873
SNP_A-1980898 AB 0.002409 AB 1196.784302 878.862671
SNP_A-1983139 AA 0.025682 AA 2868.540771 810.013306
SNP_A-4265735 AA 0.008104 AA 2155.083984 476.827179
SNP_A-1995832 BB 0.002658 BB 628.249817 1922.447510
SNP_A-1995893 BB 0.006540 BB 477.819794 2599.705322
SNP_A-1997689 BB 0.009998 BB 903.720154 3780.957764
SNP_A-1997709 AA 0.003233 AA 1921.538696 284.342224
SNP_A-1997896 BB 0.002509 BB 613.527649 3498.246826
SNP_A-1997922 AA 0.022005 AA 1860.631714 348.478455
SNP_A-2000230 AA 0.008663 AA 2708.731445 1333.913574
SNP_A-2000332 AA 0.021730 AA 4373.803223 1270.184937
SNP_A-2000337 AA 0.016550 AA 1728.474854 394.413361
SNP_A-2000342 AA 0.008015 AA 4072.052490 976.993408
SNP_A-4268172 AA 0.004381 AA 958.146667 335.681244

Total number of rows: 934968

Table truncated, full table size 47497 Kbytes.




Supplementary file Size Download File type/resource
GSM917340_MT674_MDT-MB-53.CEL.gz 29.8 Mb (ftp)(http) CEL
GSM917340_MT674_MDT-MB-53.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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