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Sample GSM917726 Query DataSets for GSM917726
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-321 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 9.0
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-321
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 0.030607 BB 604.950989 1594.799194
SNP_A-1967418 BB 0.003542 BB 260.297638 638.378845
SNP_A-1969580 BB 0.008439 BB 1331.712891 3801.279785
SNP_A-4263484 BB 0.011951 BB 430.309601 1194.764404
SNP_A-1978185 AA 0.011879 AA 742.569153 248.566742
SNP_A-4264431 AA 0.004013 AA 2180.224854 356.399200
SNP_A-1980898 AA 0.007143 AA 1380.652100 267.478729
SNP_A-1983139 AA 0.027455 AA 684.674683 283.573242
SNP_A-4265735 AA 0.041801 AA 1058.595459 435.316772
SNP_A-1995832 NC 0.635955 AA 1184.001099 397.609253
SNP_A-1995893 NC 0.326152 AA 1345.517212 786.214661
SNP_A-1997689 BB 0.019686 BB 535.734253 1747.504517
SNP_A-1997709 AA 0.007767 AA 1234.917603 272.835724
SNP_A-1997896 AA 0.011886 AA 1464.014648 448.503906
SNP_A-1997922 AA 0.010149 AA 938.738708 255.761719
SNP_A-2000230 AA 0.014206 AA 1734.856689 754.822998
SNP_A-2000332 AA 0.015678 AA 2453.975830 577.665405
SNP_A-2000337 AA 0.007494 AA 1204.581909 255.761719
SNP_A-2000342 AA 0.016761 AA 2348.641602 692.568970
SNP_A-4268172 BB 0.003249 BB 266.640991 1386.519775

Total number of rows: 934968

Table truncated, full table size 47486 Kbytes.




Supplementary file Size Download File type/resource
GSM917726_MT22_MDT-MB-321.CEL.gz 30.1 Mb (ftp)(http) CEL
GSM917726_MT22_MDT-MB-321.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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