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Sample GSM917640 Query DataSets for GSM917640
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-176 [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-176
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 0.005103 BB 573.477173 1907.392212
SNP_A-1967418 AB 0.011286 AB 425.742188 483.274719
SNP_A-1969580 BB 0.001231 BB 1546.896729 4930.913086
SNP_A-4263484 AB 0.010614 AB 1078.137939 730.988464
SNP_A-1978185 AA 0.003744 AA 998.592407 260.959045
SNP_A-4264431 AA 0.015377 AA 1652.412842 318.982269
SNP_A-1980898 BB 0.003690 BB 274.818939 1184.026855
SNP_A-1983139 AA 0.010001 AA 1374.437988 271.958374
SNP_A-4265735 AB 0.009626 AB 636.656982 778.544434
SNP_A-1995832 BB 0.002043 BB 449.731140 1739.282227
SNP_A-1995893 BB 0.010717 BB 411.851959 1654.613403
SNP_A-1997689 BB 0.005716 BB 557.114990 2425.833496
SNP_A-1997709 AA 0.005843 AA 1407.227783 217.336639
SNP_A-1997896 AB 0.007206 AB 1298.765259 1645.905396
SNP_A-1997922 AB 0.017744 AB 608.956116 604.830078
SNP_A-2000230 AA 0.020461 AA 1541.770752 762.491699
SNP_A-2000332 AA 0.003421 AA 3052.864990 703.023315
SNP_A-2000337 AA 0.004524 AA 1792.130005 245.100418
SNP_A-2000342 AA 0.013582 AA 2556.723145 604.830078
SNP_A-4268172 AA 0.027883 AA 421.046356 307.130920

Total number of rows: 934968

Table truncated, full table size 47477 Kbytes.




Supplementary file Size Download File type/resource
GSM917640_MT368_MDT-MB-176.CEL.gz 29.3 Mb (ftp)(http) CEL
GSM917640_MT368_MDT-MB-176.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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