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Sample GSM917613 Query DataSets for GSM917613
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-141 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 6.0
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-141
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 AB 0.001737 AB 1588.041138 1784.630493
SNP_A-1967418 BB 0.003156 BB 292.836945 896.913208
SNP_A-1969580 BB 0.001333 BB 1523.045532 5000.020508
SNP_A-4263484 BB 0.005999 BB 399.397858 1359.447876
SNP_A-1978185 AA 0.003232 AA 1021.986328 277.167511
SNP_A-4264431 AA 0.004322 AA 3040.097412 423.466431
SNP_A-1980898 BB 0.001229 BB 281.059418 1528.242554
SNP_A-1983139 AA 0.000770 AA 1592.186279 483.257507
SNP_A-4265735 AA 0.000523 AA 1606.766479 389.695129
SNP_A-1995832 AA 0.001332 AA 2119.929443 425.915558
SNP_A-1995893 AA 0.003781 AA 2510.152588 936.597351
SNP_A-1997689 BB 0.002710 BB 540.140564 2849.091797
SNP_A-1997709 AA 0.007795 AA 2114.845703 282.407043
SNP_A-1997896 AA 0.000868 AA 2216.801758 471.647949
SNP_A-1997922 AA 0.002841 AA 1457.200684 285.920074
SNP_A-2000230 AA 0.003653 AA 2253.906250 864.591980
SNP_A-2000332 AB 0.004278 AB 2847.461914 2759.399170
SNP_A-2000337 AA 0.001648 AA 1551.861572 259.701965
SNP_A-2000342 AA 0.006023 AA 3890.621582 1039.537109
SNP_A-4268172 AB 0.022484 AB 486.286163 1017.242004

Total number of rows: 934968

Table truncated, full table size 47485 Kbytes.




Supplementary file Size Download File type/resource
GSM917613_MT328_MDT-MB-141.CEL.gz 30.2 Mb (ftp)(http) CEL
GSM917613_MT328_MDT-MB-141.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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