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Sample GSM917681 Query DataSets for GSM917681
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-200 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 5.2
gender: F
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-200
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 0.003758 BB 597.566162 2891.401855
SNP_A-1967418 BB 0.008190 BB 255.902985 546.981567
SNP_A-1969580 BB 0.003077 BB 1711.807617 5175.979980
SNP_A-4263484 AB 0.000893 AB 1622.315796 1168.813843
SNP_A-1978185 AA 0.000106 AA 1247.127319 330.090881
SNP_A-4264431 AA 0.010246 AA 1874.766357 361.287415
SNP_A-1980898 AB 0.003638 AB 1046.724854 717.762634
SNP_A-1983139 AA 0.004693 AA 1986.427246 625.745178
SNP_A-4265735 AB 0.002451 AB 929.676086 918.248535
SNP_A-1995832 BB 0.008233 BB 526.680725 2200.904785
SNP_A-1995893 BB 0.010733 BB 406.400879 2656.762207
SNP_A-1997689 BB 0.003317 BB 681.914124 3575.857422
SNP_A-1997709 AA 0.000986 AA 1661.623535 259.969727
SNP_A-1997896 AB 0.002563 AB 1650.498291 2068.779053
SNP_A-1997922 AB 0.006549 AB 717.762634 820.704163
SNP_A-2000230 AA 0.015845 AA 1944.844482 1175.801270
SNP_A-2000332 AB 0.001443 AB 2651.943359 2605.080811
SNP_A-2000337 AA 0.006983 AA 1480.392944 349.848663
SNP_A-2000342 AA 0.000348 AA 3435.314697 880.589905
SNP_A-4268172 AA 0.007095 AA 521.651672 240.000244

Total number of rows: 934968

Table truncated, full table size 47477 Kbytes.




Supplementary file Size Download File type/resource
GSM917681_MT392_MDT-MB-200.CEL.gz 29.5 Mb (ftp)(http) CEL
GSM917681_MT392_MDT-MB-200.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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