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Sample GSM917634 Query DataSets for GSM917634
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-167 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 4.0
gender: M
histological subtype: Classic
subgroup: Group 3
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-167
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 0.001585 BB 663.720642 2713.788818
SNP_A-1967418 BB 0.001256 BB 266.181152 713.905823
SNP_A-1969580 BB 0.003852 BB 1188.018188 4695.124512
SNP_A-4263484 BB 0.001973 BB 412.107483 1724.270630
SNP_A-1978185 AA 0.006877 AA 1602.826172 407.410034
SNP_A-4264431 AA 0.007357 AA 1984.026489 251.067444
SNP_A-1980898 BB 0.004456 BB 235.113113 1136.392090
SNP_A-1983139 AA 0.000835 AA 1645.821045 453.974335
SNP_A-4265735 AA 0.008415 AA 1136.392090 320.641846
SNP_A-1995832 AB 0.010486 AB 1769.951660 1470.212769
SNP_A-1995893 AB 0.006725 AB 1772.012817 1652.936890
SNP_A-1997689 BB 0.000192 BB 637.792908 3092.457275
SNP_A-1997709 AA 0.007402 AA 1893.566162 339.580963
SNP_A-1997896 AB 0.002981 AB 1302.215210 2144.677246
SNP_A-1997922 AA 0.001551 AA 1215.498535 258.623657
SNP_A-2000230 AA 0.009008 AA 2067.852539 720.329895
SNP_A-2000332 AA 0.001670 AA 3616.983887 884.967346
SNP_A-2000337 AA 0.015384 AA 998.322266 312.773041
SNP_A-2000342 AA 0.003213 AA 3204.007812 958.404968
SNP_A-4268172 AA 0.001395 AA 709.984619 247.363937

Total number of rows: 934968

Table truncated, full table size 47471 Kbytes.




Supplementary file Size Download File type/resource
GSM917634_MT360_MDT-MB-167.CEL.gz 29.0 Mb (ftp)(http) CEL
GSM917634_MT360_MDT-MB-167.birdseed.chp.gz 13.4 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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