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Sample GSM917436 Query DataSets for GSM917436
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-131 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 10.0
gender: F
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-131
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 0.003763 BB 682.304016 2140.967529
SNP_A-1967418 BB 0.004976 BB 300.307892 945.467834
SNP_A-1969580 BB 0.002268 BB 1620.128052 4902.871094
SNP_A-4263484 AB 0.095364 AB 1117.244507 297.759247
SNP_A-1978185 AA 0.003116 AA 1164.727905 401.507965
SNP_A-4264431 AA 0.005579 AA 2858.348877 526.823486
SNP_A-1980898 BB 0.000829 BB 279.510132 1480.020996
SNP_A-1983139 AA 0.001387 AA 1555.218384 429.570068
SNP_A-4265735 AB 0.010754 AB 1206.624756 784.896484
SNP_A-1995832 BB 0.000900 BB 486.771637 1701.923828
SNP_A-1995893 BB 0.002357 BB 471.614014 2390.356445
SNP_A-1997689 BB 0.013372 BB 737.055969 2282.876465
SNP_A-1997709 AA 0.015135 AA 1211.640381 313.051422
SNP_A-1997896 AB 0.012182 AB 1655.278442 1590.725830
SNP_A-1997922 AB 0.054229 AB 967.079712 1376.424805
SNP_A-2000230 AA 0.006225 AA 2679.409668 1275.611938
SNP_A-2000332 AA 0.005511 AA 2945.230957 859.994263
SNP_A-2000337 AA 0.019877 AA 1149.405273 184.783127
SNP_A-2000342 AA 0.000611 AA 3416.649414 905.922546
SNP_A-4268172 AA 0.001786 AA 864.893250 296.165283

Total number of rows: 934968

Table truncated, full table size 47492 Kbytes.




Supplementary file Size Download File type/resource
GSM917436_MT318_MDT-MB-131.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM917436_MT318_MDT-MB-131.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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