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Sample GSM917611 Query DataSets for GSM917611
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-139 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 9.0
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-139
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 0.010516 AB 1068.137939 944.664490
SNP_A-1967418 BB 0.003500 BB 227.590927 655.350403
SNP_A-1969580 BB 0.005611 BB 1753.334961 4863.477051
SNP_A-4263484 NC 0.174601 BB 382.564545 751.157532
SNP_A-1978185 AA 0.002494 AA 1104.103027 241.898529
SNP_A-4264431 AA 0.004759 AA 2970.445068 358.460663
SNP_A-1980898 AB 0.004405 AB 919.677246 674.568420
SNP_A-1983139 AA 0.003118 AA 1398.298950 379.385376
SNP_A-4265735 AB 0.002495 AB 1026.836548 911.855530
SNP_A-1995832 BB 0.004060 BB 454.101715 1922.578247
SNP_A-1995893 BB 0.008485 BB 405.978333 1713.635742
SNP_A-1997689 BB 0.015567 BB 442.473206 1902.633667
SNP_A-1997709 AA 0.012426 AA 1089.332397 206.341385
SNP_A-1997896 AB 0.000678 AB 1530.838379 2094.209961
SNP_A-1997922 AB 0.010611 AB 688.244202 678.042358
SNP_A-2000230 AA 0.018932 AA 1756.794312 602.090698
SNP_A-2000332 AB 0.001923 AB 2599.886719 2751.539062
SNP_A-2000337 AA 0.014059 AA 1134.492676 215.208603
SNP_A-2000342 AA 0.006441 AA 2820.937500 866.185669
SNP_A-4268172 AA 0.002329 AA 657.970276 248.851135

Total number of rows: 934968

Table truncated, full table size 47494 Kbytes.




Supplementary file Size Download File type/resource
GSM917611_MT326_MDT-MB-139.CEL.gz 29.5 Mb (ftp)(http) CEL
GSM917611_MT326_MDT-MB-139.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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