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Sample GSM917300 Query DataSets for GSM917300
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-5 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 6.5
gender: M
histological subtype: Classic
subgroup: Group 4
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-5
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 0.003962 BB 572.842285 1976.313599
SNP_A-1967418 BB 0.004123 BB 280.661865 642.974365
SNP_A-1969580 BB 0.000697 BB 1313.234497 4497.043457
SNP_A-4263484 AB 0.009566 AB 1069.138184 836.027344
SNP_A-1978185 AA 0.006070 AA 907.066223 277.604523
SNP_A-4264431 AA 0.004551 AA 2415.860596 461.052338
SNP_A-1980898 AA 0.000685 AA 1666.589111 246.097641
SNP_A-1983139 AA 0.012270 AA 2371.009033 736.442078
SNP_A-4265735 AB 0.048167 AB 2015.028809 1313.234497
SNP_A-1995832 BB 0.002739 BB 558.954346 1982.568481
SNP_A-1995893 BB 0.007806 BB 543.894958 1959.303223
SNP_A-1997689 BB 0.006060 BB 617.230469 2432.372070
SNP_A-1997709 AA 0.005482 AA 1329.933838 276.081512
SNP_A-1997896 AB 0.008207 AB 1794.464966 1901.953369
SNP_A-1997922 AB 0.005537 AB 844.906311 1044.473755
SNP_A-2000230 AA 0.007007 AA 2050.052979 801.257935
SNP_A-2000332 BB 0.003584 BB 1326.541382 3458.037842
SNP_A-2000337 AA 0.012194 AA 1137.628174 335.911652
SNP_A-2000342 AA 0.009584 AA 2617.579102 737.973999
SNP_A-4268172 AA 0.001669 AA 832.300049 264.501221

Total number of rows: 934968

Table truncated, full table size 47502 Kbytes.




Supplementary file Size Download File type/resource
GSM917300_MT632_MDT-MB-5.CEL.gz 28.7 Mb (ftp)(http) CEL
GSM917300_MT632_MDT-MB-5.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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