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Sample GSM917369 Query DataSets for GSM917369
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-62 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 12.0
gender: M
histological subtype: Classic
subgroup: N/A
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-62
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 0.023399 AB 2572.592041 2647.197754
SNP_A-1967418 BB 0.069158 BB 385.269470 1440.369995
SNP_A-1969580 BB 0.025851 BB 2264.501953 6964.623535
SNP_A-4263484 AB 0.034561 AB 2814.999756 1706.241699
SNP_A-1978185 AA 0.021103 AA 1882.435913 377.879150
SNP_A-4264431 AA 0.015896 AA 3510.569824 412.670166
SNP_A-1980898 AB 0.055706 AB 1954.526245 1577.373535
SNP_A-1983139 AA 0.012809 AA 2556.388184 640.607605
SNP_A-4265735 AB 0.009111 AB 1342.495361 1469.475708
SNP_A-1995832 BB 0.008144 BB 583.286499 2239.179443
SNP_A-1995893 BB 0.026369 BB 377.879150 1334.207275
SNP_A-1997689 AB 0.006076 AB 3012.339600 2561.504150
SNP_A-1997709 AB 0.010917 AB 849.388611 814.784790
SNP_A-1997896 AA 0.001583 AA 2059.385742 535.956116
SNP_A-1997922 BB 0.003327 BB 594.828247 1618.023560
SNP_A-2000230 AA 0.002695 AA 2814.874023 1011.878662
SNP_A-2000332 BB 0.001164 BB 1163.722046 3844.583252
SNP_A-2000337 AA 0.032127 AA 2422.884766 334.676910
SNP_A-2000342 AA 0.004114 AA 3780.361328 998.471313
SNP_A-4268172 AA 0.002344 AA 862.706604 267.156921

Total number of rows: 934968

Table truncated, full table size 47498 Kbytes.




Supplementary file Size Download File type/resource
GSM917369_MT680_MDT-MB-62.CEL.gz 29.5 Mb (ftp)(http) CEL
GSM917369_MT680_MDT-MB-62.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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