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Sample GSM917424 Query DataSets for GSM917424
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-118 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 8.8
gender: M
histological subtype: Large Cell/Anaplastic
subgroup: SHH
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-118
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 0.000783 BB 634.031189 2380.171631
SNP_A-1967418 BB 0.002876 BB 291.068268 693.448303
SNP_A-1969580 BB 0.001315 BB 1243.942017 4378.647949
SNP_A-4263484 BB 0.003227 BB 355.189545 1585.066650
SNP_A-1978185 AA 0.004406 AA 1448.749878 292.596283
SNP_A-4264431 AB 0.006364 AB 2071.483154 1336.815430
SNP_A-1980898 BB 0.001589 BB 267.366150 1323.587036
SNP_A-1983139 AA 0.002395 AA 1402.503662 451.451447
SNP_A-4265735 BB 0.004052 BB 390.739349 1736.749512
SNP_A-1995832 BB 0.003951 BB 441.574951 1887.251953
SNP_A-1995893 BB 0.007951 BB 584.763245 2637.398193
SNP_A-1997689 BB 0.001902 BB 599.578979 3258.572266
SNP_A-1997709 AA 0.004739 AA 1640.598389 226.477417
SNP_A-1997896 AA 0.002900 AA 2368.709717 458.020660
SNP_A-1997922 BB 0.008469 BB 699.884155 1711.333618
SNP_A-2000230 AA 0.001641 AA 2381.218018 942.387756
SNP_A-2000332 AB 0.006339 AB 2846.818604 2983.893311
SNP_A-2000337 AA 0.004136 AA 1402.449463 318.857697
SNP_A-2000342 AA 0.009107 AA 3828.194336 1141.358032
SNP_A-4268172 AA 0.003456 AA 642.202576 209.400070

Total number of rows: 934968

Table truncated, full table size 47483 Kbytes.




Supplementary file Size Download File type/resource
GSM917424_MT299_MDT-MB-118.CEL.gz 28.2 Mb (ftp)(http) CEL
GSM917424_MT299_MDT-MB-118.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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