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Sample GSM917614 Query DataSets for GSM917614
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-142 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 9.0
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-142
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 0.002716 BB 488.388855 2055.108398
SNP_A-1967418 BB 0.004532 BB 303.670502 674.413025
SNP_A-1969580 BB 0.007884 BB 1119.897461 3560.927002
SNP_A-4263484 BB 0.012956 BB 315.059387 1107.219727
SNP_A-1978185 AA 0.004548 AA 1031.624512 365.682037
SNP_A-4264431 AA 0.000511 AA 2633.255615 401.124939
SNP_A-1980898 BB 0.003576 BB 226.342438 1200.855469
SNP_A-1983139 AA 0.004226 AA 1322.876587 353.828766
SNP_A-4265735 AB 0.000418 AB 1075.475952 1096.324951
SNP_A-1995832 AB 0.001637 AB 1356.262695 1026.145996
SNP_A-1995893 AB 0.002208 AB 1308.286133 1483.213379
SNP_A-1997689 BB 0.002436 BB 682.403198 2857.174072
SNP_A-1997709 AA 0.003212 AA 1403.096802 258.823303
SNP_A-1997896 AA 0.006023 AA 1676.066406 422.776642
SNP_A-1997922 AB 0.003171 AB 1060.042480 1019.791504
SNP_A-2000230 AA 0.007503 AA 2512.134033 1279.957153
SNP_A-2000332 AA 0.000890 AA 3417.396729 871.906250
SNP_A-2000337 AA 0.009630 AA 1112.665771 288.527802
SNP_A-2000342 AA 0.006727 AA 3641.106201 1102.680298
SNP_A-4268172 AB 0.001982 AB 556.375793 955.457397

Total number of rows: 934968

Table truncated, full table size 47483 Kbytes.




Supplementary file Size Download File type/resource
GSM917614_MT329_MDT-MB-142.CEL.gz 29.8 Mb (ftp)(http) CEL
GSM917614_MT329_MDT-MB-142.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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