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Sample GSM917711 Query DataSets for GSM917711
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-304 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 11.0
gender: M
histological subtype: Classic
subgroup: WNT
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-304
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 0.005845 BB 780.594604 2204.804688
SNP_A-1967418 BB 0.001748 BB 252.108658 820.401733
SNP_A-1969580 BB 0.013786 BB 1986.444702 6343.377441
SNP_A-4263484 BB 0.003617 BB 644.409607 2093.455322
SNP_A-1978185 AA 0.002153 AA 1297.269531 270.360352
SNP_A-4264431 AA 0.008700 AA 3080.121826 567.561035
SNP_A-1980898 BB 0.001881 BB 274.468414 1563.403076
SNP_A-1983139 AB 0.001427 AB 726.909119 748.748840
SNP_A-4265735 AA 0.002524 AA 1857.924072 419.700592
SNP_A-1995832 BB 0.005582 BB 439.685547 1973.360596
SNP_A-1995893 BB 0.002666 BB 503.065643 2127.198242
SNP_A-1997689 BB 0.008378 BB 428.862701 3084.074951
SNP_A-1997709 AA 0.002425 AA 1637.559814 244.006332
SNP_A-1997896 AB 0.022582 AB 2149.263672 2832.409912
SNP_A-1997922 AB 0.002437 AB 1031.399902 1007.177795
SNP_A-2000230 AA 0.004220 AA 2740.047852 890.509277
SNP_A-2000332 AA 0.003907 AA 3738.050537 723.259949
SNP_A-2000337 AA 0.007419 AA 1581.713135 210.386978
SNP_A-2000342 AA 0.020263 AA 3629.846680 1289.020020
SNP_A-4268172 AA 0.011563 AA 1093.837524 301.324829

Total number of rows: 934968

Table truncated, full table size 47499 Kbytes.




Supplementary file Size Download File type/resource
GSM917711_MT5_MDT-MB-304.CEL.gz 29.4 Mb (ftp)(http) CEL
GSM917711_MT5_MDT-MB-304.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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