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Sample GSM917748 Query DataSets for GSM917748
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-328 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 10.0
gender: M
histological subtype: Classic
subgroup: WNT
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-328
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 0.004432 BB 547.924866 1922.650757
SNP_A-1967418 BB 0.009961 BB 278.581299 1032.985596
SNP_A-1969580 BB 0.012014 BB 2103.392578 6182.629883
SNP_A-4263484 AB 0.003352 AB 1971.598389 1254.929810
SNP_A-1978185 AA 0.002963 AA 1035.851929 284.644897
SNP_A-4264431 AA 0.008476 AA 3277.523682 435.835632
SNP_A-1980898 BB 0.013025 BB 370.180542 2103.392578
SNP_A-1983139 AA 0.002685 AA 1429.416504 390.610718
SNP_A-4265735 BB 0.005653 BB 661.136780 1885.405396
SNP_A-1995832 AB 0.004113 AB 1529.974243 1370.714966
SNP_A-1995893 AB 0.004660 AB 1409.980469 1331.518555
SNP_A-1997689 BB 0.003599 BB 595.314697 3441.835693
SNP_A-1997709 AA 0.001598 AA 1808.359497 286.358093
SNP_A-1997896 AB 0.015015 AB 1856.652100 2888.883057
SNP_A-1997922 AA 0.007672 AA 1620.710938 320.002441
SNP_A-2000230 AA 0.008520 AA 2971.948730 878.901428
SNP_A-2000332 AA 0.008164 AA 4041.791748 763.747131
SNP_A-2000337 AA 0.008886 AA 2036.153931 302.766754
SNP_A-2000342 AA 0.007403 AA 3854.009766 1097.666138
SNP_A-4268172 AA 0.035319 AA 1338.608276 338.892914

Total number of rows: 934968

Table truncated, full table size 47498 Kbytes.




Supplementary file Size Download File type/resource
GSM917748_MT29_MDT-MB-328.CEL.gz 29.6 Mb (ftp)(http) CEL
GSM917748_MT29_MDT-MB-328.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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