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Sample GSM917688 Query DataSets for GSM917688
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-208 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 6.6
gender: F
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-208
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 0.038556 BB 686.373474 4173.608398
SNP_A-1967418 BB 0.001729 BB 261.618042 837.341797
SNP_A-1969580 BB 0.002145 BB 1164.258667 4241.220215
SNP_A-4263484 BB 0.006857 BB 633.172607 2250.661621
SNP_A-1978185 AA 0.007531 AA 1553.740601 292.508484
SNP_A-4264431 AB 0.001385 AB 1552.704590 1278.026855
SNP_A-1980898 BB 0.002649 BB 288.258270 1252.298096
SNP_A-1983139 AA 0.007838 AA 1167.224609 455.521484
SNP_A-4265735 AB 0.001713 AB 1205.643188 1105.748535
SNP_A-1995832 AB 0.003468 AB 1532.406738 1332.620483
SNP_A-1995893 AB 0.008580 AB 1831.005737 1885.489136
SNP_A-1997689 BB 0.006256 BB 794.177185 3800.342041
SNP_A-1997709 AA 0.001396 AA 1793.297363 284.479431
SNP_A-1997896 AA 0.003954 AA 1844.189453 517.660034
SNP_A-1997922 AB 0.004757 AB 795.291321 763.817261
SNP_A-2000230 AA 0.001597 AA 2364.611328 998.531982
SNP_A-2000332 AB 0.002885 AB 2221.647705 2482.430420
SNP_A-2000337 AA 0.001318 AA 1691.031860 292.508484
SNP_A-2000342 AA 0.004204 AA 3343.502197 1021.121521
SNP_A-4268172 AA 0.002246 AA 692.698364 304.145752

Total number of rows: 934968

Table truncated, full table size 47474 Kbytes.




Supplementary file Size Download File type/resource
GSM917688_MT399_MDT-MB-208.CEL.gz 29.4 Mb (ftp)(http) CEL
GSM917688_MT399_MDT-MB-208.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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