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Sample GSM917723 Query DataSets for GSM917723
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-318 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 16.0
gender: F
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-318
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 0.001087 BB 608.671753 2293.470215
SNP_A-1967418 BB 0.004657 BB 292.064423 939.003174
SNP_A-1969580 BB 0.004659 BB 1609.100830 5472.370605
SNP_A-4263484 BB 0.007278 BB 673.111633 2279.647949
SNP_A-1978185 AA 0.002113 AA 1124.265869 251.186035
SNP_A-4264431 AA 0.011430 AA 3377.416016 548.619873
SNP_A-1980898 AB 0.007252 AB 1366.864868 1173.197510
SNP_A-1983139 AA 0.004282 AA 1229.876587 405.877289
SNP_A-4265735 AB 0.001737 AB 960.310486 1059.218140
SNP_A-1995832 AB 0.004032 AB 1310.437988 1322.938843
SNP_A-1995893 AB 0.002798 AB 1274.897339 1542.793457
SNP_A-1997689 BB 0.001522 BB 580.404236 3060.890869
SNP_A-1997709 AA 0.000566 AA 1654.369995 264.724121
SNP_A-1997896 AB 0.006715 AB 1853.419067 2459.173584
SNP_A-1997922 AA 0.000296 AA 1289.324829 278.358795
SNP_A-2000230 AA 0.005364 AA 2814.517334 886.560181
SNP_A-2000332 AA 0.003743 AA 3482.317383 622.927368
SNP_A-2000337 AA 0.009839 AA 1721.512085 200.744293
SNP_A-2000342 AA 0.010524 AA 3783.994141 1171.291992
SNP_A-4268172 NC 0.787407 AB 678.306274 1378.527100

Total number of rows: 934968

Table truncated, full table size 47492 Kbytes.




Supplementary file Size Download File type/resource
GSM917723_MT19_MDT-MB-318.CEL.gz 29.7 Mb (ftp)(http) CEL
GSM917723_MT19_MDT-MB-318.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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