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Sample GSM917437 Query DataSets for GSM917437
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-132 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 7.0
gender: F
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-132
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 0.005273 BB 614.102600 1946.189209
SNP_A-1967418 BB 0.002797 BB 249.892868 658.225281
SNP_A-1969580 BB 0.013240 BB 2032.725830 5128.353027
SNP_A-4263484 BB 0.009307 BB 414.513702 1253.221680
SNP_A-1978185 AA 0.005766 AA 1508.756470 301.394073
SNP_A-4264431 AA 0.004608 AA 2328.092529 439.613373
SNP_A-1980898 AB 0.001009 AB 1072.190308 961.203125
SNP_A-1983139 AA 0.003366 AA 1322.198120 382.268066
SNP_A-4265735 AA 0.003772 AA 1369.966431 389.644409
SNP_A-1995832 BB 0.003769 BB 494.129883 1452.423462
SNP_A-1995893 BB 0.006834 BB 337.811523 1743.875122
SNP_A-1997689 BB 0.005159 BB 599.076965 2481.761963
SNP_A-1997709 AA 0.007300 AA 1209.043335 249.892868
SNP_A-1997896 BB 0.003787 BB 632.863647 2919.763428
SNP_A-1997922 AA 0.000779 AA 1282.368042 302.975983
SNP_A-2000230 AA 0.002837 AA 2441.052490 868.424561
SNP_A-2000332 AB 0.002102 AB 2410.221191 2319.933594
SNP_A-2000337 AA 0.002700 AA 1742.380005 259.562286
SNP_A-2000342 AA 0.003293 AA 3720.510254 979.856873
SNP_A-4268172 AA 0.000554 AA 806.056702 291.699249

Total number of rows: 934968

Table truncated, full table size 47492 Kbytes.




Supplementary file Size Download File type/resource
GSM917437_MT319_MDT-MB-132.CEL.gz 30.6 Mb (ftp)(http) CEL
GSM917437_MT319_MDT-MB-132.birdseed.chp.gz 13.6 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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