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Sample GSM917646 Query DataSets for GSM917646
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-182 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 5.0
gender: M
histological subtype: Large Cell/Anaplastic
subgroup: Group 3
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-182
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 0.006297 BB 684.575623 3161.032227
SNP_A-1967418 BB 0.002091 BB 233.130692 754.806152
SNP_A-1969580 BB 0.003548 BB 1745.224731 5289.761719
SNP_A-4263484 AA 0.000673 AA 2530.963623 377.521149
SNP_A-1978185 AA 0.002310 AA 1184.737671 387.752411
SNP_A-4264431 AB 0.015708 AB 1005.709229 900.192993
SNP_A-1980898 BB 0.001367 BB 266.939850 1347.596313
SNP_A-1983139 AA 0.000882 AA 1572.048462 478.740997
SNP_A-4265735 AA 0.006720 AA 1235.238403 377.521149
SNP_A-1995832 AA 0.013728 AA 2633.170410 511.658722
SNP_A-1995893 AA 0.003094 AA 2426.105225 886.006226
SNP_A-1997689 BB 0.001261 BB 592.481018 3092.728760
SNP_A-1997709 AA 0.007583 AA 2121.833984 290.955261
SNP_A-1997896 AA 0.004068 AA 1784.305908 441.592133
SNP_A-1997922 AA 0.006455 AA 1029.523804 272.934052
SNP_A-2000230 AA 0.015370 AA 1668.311157 833.774963
SNP_A-2000332 AA 0.001606 AA 3369.275391 903.139038
SNP_A-2000337 AA 0.001066 AA 1676.920654 276.777283
SNP_A-2000342 AA 0.005440 AA 2857.385742 839.941040
SNP_A-4268172 AB 0.007287 AB 403.103394 664.767944

Total number of rows: 934968

Table truncated, full table size 47473 Kbytes.




Supplementary file Size Download File type/resource
GSM917646_MT374_MDT-MB-182.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM917646_MT374_MDT-MB-182.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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