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Sample GSM917705 Query DataSets for GSM917705
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-228 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: N/A
gender: M
histological subtype: Medulloblastoma
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-228
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 0.000648 BB 607.443665 2352.696777
SNP_A-1967418 AA 0.008732 AA 1055.356689 223.560043
SNP_A-1969580 BB 0.004069 BB 1457.263428 5236.506348
SNP_A-4263484 AB 0.001733 AB 1767.737793 1098.272949
SNP_A-1978185 AA 0.008340 AA 853.922424 305.535706
SNP_A-4264431 AB 0.004429 AB 1944.490723 1258.872192
SNP_A-1980898 BB 0.001024 BB 269.148712 1395.271118
SNP_A-1983139 AA 0.002173 AA 1924.496826 557.718018
SNP_A-4265735 AB 0.001457 AB 1191.439941 1146.670044
SNP_A-1995832 AB 0.001915 AB 1482.033936 1124.801636
SNP_A-1995893 AB 0.005886 AB 1664.822876 1492.075317
SNP_A-1997689 BB 0.006816 BB 791.685608 2840.563965
SNP_A-1997709 AA 0.002255 AA 1562.450439 244.254990
SNP_A-1997896 AB 0.000442 AB 1508.848755 2199.406738
SNP_A-1997922 AA 0.004027 AA 1415.524292 228.400085
SNP_A-2000230 AA 0.003229 AA 2245.776367 1019.967651
SNP_A-2000332 AB 0.006716 AB 2943.224609 2899.996826
SNP_A-2000337 AA 0.001768 AA 1734.778931 281.007751
SNP_A-2000342 AA 0.000948 AA 3432.879883 836.287659
SNP_A-4268172 AA 0.002188 AA 695.876221 225.822784

Total number of rows: 934968

Table truncated, full table size 47482 Kbytes.




Supplementary file Size Download File type/resource
GSM917705_MT417_MDT-MB-228.CEL.gz 29.1 Mb (ftp)(http) CEL
GSM917705_MT417_MDT-MB-228.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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