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Sample GSM917680 Query DataSets for GSM917680
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-199 [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: 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-199
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 0.004961 BB 506.366669 2845.827393
SNP_A-1967418 BB 0.007266 BB 220.731583 557.505493
SNP_A-1969580 BB 0.013272 BB 1235.078735 3435.509277
SNP_A-4263484 AB 0.001920 AB 1620.435791 1009.752136
SNP_A-1978185 AA 0.002224 AA 1076.503418 286.443573
SNP_A-4264431 AB 0.020524 AB 1039.124023 740.602234
SNP_A-1980898 BB 0.004358 BB 264.524048 1144.273926
SNP_A-1983139 AA 0.021003 AA 739.059998 293.978546
SNP_A-4265735 AA 0.001363 AA 1536.645142 409.337189
SNP_A-1995832 AB 0.003588 AB 1544.764771 1099.364624
SNP_A-1995893 AB 0.005653 AB 1659.832520 1906.685547
SNP_A-1997689 BB 0.004402 BB 553.720337 3376.662109
SNP_A-1997709 AA 0.003795 AA 1840.182617 253.209152
SNP_A-1997896 AA 0.003539 AA 1819.909424 454.160553
SNP_A-1997922 AB 0.002539 AB 945.976196 804.826416
SNP_A-2000230 AA 0.005327 AA 2078.435059 908.916565
SNP_A-2000332 AA 0.001728 AA 3555.969238 744.387451
SNP_A-2000337 AA 0.003695 AA 1424.644165 247.689987
SNP_A-2000342 AA 0.003093 AA 3190.533691 949.629150
SNP_A-4268172 AA 0.000529 AA 780.273315 269.748199

Total number of rows: 934968

Table truncated, full table size 47473 Kbytes.




Supplementary file Size Download File type/resource
GSM917680_MT391_MDT-MB-199.CEL.gz 30.3 Mb (ftp)(http) CEL
GSM917680_MT391_MDT-MB-199.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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