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Sample GSM917304 Query DataSets for GSM917304
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-9 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 3.2
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-9
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 0.012200 BB 486.451782 1596.355713
SNP_A-1967418 AB 0.002841 AB 549.204895 550.073914
SNP_A-1969580 BB 0.001247 BB 1548.907349 4925.745117
SNP_A-4263484 AB 0.006791 AB 1239.279297 809.921326
SNP_A-1978185 AA 0.005801 AA 912.451111 257.092316
SNP_A-4264431 AB 0.004468 AB 1358.533325 1241.918091
SNP_A-1980898 BB 0.000336 BB 315.235107 1504.820190
SNP_A-1983139 AA 0.001607 AA 1648.743652 523.493530
SNP_A-4265735 AB 0.001818 AB 1217.895020 1137.192505
SNP_A-1995832 BB 0.005261 BB 453.990631 1985.989014
SNP_A-1995893 BB 0.007190 BB 448.450348 1801.845337
SNP_A-1997689 BB 0.014595 BB 503.065582 1921.754395
SNP_A-1997709 AA 0.006044 AA 1373.697266 292.077301
SNP_A-1997896 BB 0.002926 BB 748.409119 3060.100342
SNP_A-1997922 AA 0.010219 AA 933.626404 230.898682
SNP_A-2000230 AA 0.010933 AA 2021.852905 682.330872
SNP_A-2000332 AB 0.006729 AB 2648.860596 3073.464600
SNP_A-2000337 AA 0.007248 AA 1649.281128 212.389130
SNP_A-2000342 AA 0.013739 AA 2470.657227 812.570740
SNP_A-4268172 AA 0.001905 AA 715.823486 229.774307

Total number of rows: 934968

Table truncated, full table size 47488 Kbytes.




Supplementary file Size Download File type/resource
GSM917304_MT636_MDT-MB-9.CEL.gz 30.0 Mb (ftp)(http) CEL
GSM917304_MT636_MDT-MB-9.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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