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Sample GSM917696 Query DataSets for GSM917696
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-217 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 7.0
gender: M
histological subtype: Classic
subgroup: N/A
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-217
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 0.004926 BB 792.640137 2300.895996
SNP_A-1967418 BB 0.003216 BB 294.171906 689.392700
SNP_A-1969580 BB 0.011550 BB 1183.294556 5186.352539
SNP_A-4263484 AB 0.002525 AB 1771.247314 1313.095947
SNP_A-1978185 AA 0.004350 AA 987.368896 314.219604
SNP_A-4264431 AA 0.002191 AA 2434.033936 307.441559
SNP_A-1980898 BB 0.005055 BB 308.829834 1156.680664
SNP_A-1983139 AA 0.003790 AA 2072.667969 541.349976
SNP_A-4265735 AA 0.004301 AA 1986.947632 455.744171
SNP_A-1995832 AA 0.007966 AA 1948.730591 654.503540
SNP_A-1995893 AA 0.002242 AA 2426.515869 936.265015
SNP_A-1997689 BB 0.005410 BB 781.138123 2923.997803
SNP_A-1997709 AA 0.010852 AA 2139.432129 260.404449
SNP_A-1997896 AA 0.002381 AA 1905.573120 470.516205
SNP_A-1997922 AA 0.001133 AA 1252.759521 300.787079
SNP_A-2000230 AA 0.000664 AA 2612.859131 1001.031799
SNP_A-2000332 AB 0.009385 AB 3002.510742 3041.615479
SNP_A-2000337 AA 0.013173 AA 1656.781860 383.476410
SNP_A-2000342 AA 0.002912 AA 3692.956055 865.410278
SNP_A-4268172 AA 0.004510 AA 588.731689 217.993866

Total number of rows: 934968

Table truncated, full table size 47479 Kbytes.




Supplementary file Size Download File type/resource
GSM917696_MT408_MDT-MB-217.CEL.gz 29.1 Mb (ftp)(http) CEL
GSM917696_MT408_MDT-MB-217.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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