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Sample GSM917683 Query DataSets for GSM917683
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-202 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 9.0
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-202
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 0.003554 BB 626.787476 2905.220703
SNP_A-1967418 BB 0.003784 BB 216.211273 781.063416
SNP_A-1969580 BB 0.002374 BB 1160.259521 4391.328125
SNP_A-4263484 BB 0.002102 BB 539.348999 1968.487061
SNP_A-1978185 AA 0.012277 AA 1705.404663 332.853333
SNP_A-4264431 AA 0.013482 AA 1736.749268 342.462677
SNP_A-1980898 BB 0.001268 BB 260.854034 1386.988647
SNP_A-1983139 AA 0.002036 AA 1637.749390 422.999329
SNP_A-4265735 AA 0.012967 AA 1056.353027 345.190674
SNP_A-1995832 AB 0.005537 AB 1599.225586 1406.104980
SNP_A-1995893 AB 0.002823 AB 1285.124390 1581.449707
SNP_A-1997689 BB 0.002725 BB 757.381592 3365.152832
SNP_A-1997709 AA 0.003637 AA 1816.734375 251.022263
SNP_A-1997896 AA 0.007180 AA 1627.205200 374.078247
SNP_A-1997922 AB 0.001414 AB 904.566345 957.995117
SNP_A-2000230 AA 0.009777 AA 2039.258789 1129.315308
SNP_A-2000332 AA 0.005828 AA 3164.170654 1012.918396
SNP_A-2000337 AA 0.003595 AA 1525.471069 325.928680
SNP_A-2000342 AA 0.003834 AA 3454.406494 739.364868
SNP_A-4268172 AB 0.010929 AB 328.236450 650.217224

Total number of rows: 934968

Table truncated, full table size 47477 Kbytes.




Supplementary file Size Download File type/resource
GSM917683_MT394_MDT-MB-202.CEL.gz 29.0 Mb (ftp)(http) CEL
GSM917683_MT394_MDT-MB-202.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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