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Sample GSM917728 Query DataSets for GSM917728
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-323 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 10.0
gender: M
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-323
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 0.001224 AB 1674.425293 1521.240356
SNP_A-1967418 BB 0.006314 BB 272.292755 967.249390
SNP_A-1969580 BB 0.004843 BB 1616.693604 5495.744629
SNP_A-4263484 AB 0.005962 AB 1953.913940 1470.584595
SNP_A-1978185 AA 0.002282 AA 1136.419312 363.966339
SNP_A-4264431 AA 0.016345 AA 3458.354492 373.140564
SNP_A-1980898 BB 0.015805 BB 376.252380 2170.005127
SNP_A-1983139 AA 0.003747 AA 1285.428223 377.011902
SNP_A-4265735 AA 0.001261 AA 1769.377563 416.009460
SNP_A-1995832 AB 0.001901 AB 1263.412964 1169.986084
SNP_A-1995893 AB 0.000276 AB 1444.811646 1612.996338
SNP_A-1997689 BB 0.003000 BB 566.067322 3267.238525
SNP_A-1997709 AA 0.001535 AA 1781.494995 269.593445
SNP_A-1997896 AB 0.001098 AB 1526.043457 2269.093262
SNP_A-1997922 AA 0.004097 AA 1482.901489 264.223816
SNP_A-2000230 AA 0.013708 AA 3141.994141 862.195007
SNP_A-2000332 AA 0.006166 AA 3332.850342 520.382874
SNP_A-2000337 AA 0.002180 AA 1569.038086 313.131378
SNP_A-2000342 AA 0.003815 AA 3652.816895 1022.547058
SNP_A-4268172 AA 0.013632 AA 1096.074341 266.492645

Total number of rows: 934968

Table truncated, full table size 47484 Kbytes.




Supplementary file Size Download File type/resource
GSM917728_MT24_MDT-MB-323.CEL.gz 28.8 Mb (ftp)(http) CEL
GSM917728_MT24_MDT-MB-323.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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