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Sample GSM917619 Query DataSets for GSM917619
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-148 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 7.0
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-148
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 0.036738 BB 536.438416 1460.925659
SNP_A-1967418 BB 0.006295 BB 338.493103 931.543945
SNP_A-1969580 BB 0.004051 BB 1740.250366 5024.354980
SNP_A-4263484 BB 0.011020 BB 395.893219 1194.019165
SNP_A-1978185 AA 0.000575 AA 1191.413818 308.102020
SNP_A-4264431 AB 0.013317 AB 2273.527588 1654.021973
SNP_A-1980898 BB 0.002689 BB 320.289948 1691.068726
SNP_A-1983139 AA 0.003081 AA 1323.236206 422.948029
SNP_A-4265735 BB 0.004409 BB 517.842163 1399.857666
SNP_A-1995832 AB 0.002311 AB 1211.561157 1046.879150
SNP_A-1995893 AB 0.000679 AB 1402.449097 1553.773315
SNP_A-1997689 BB 0.005782 BB 652.966187 2502.124512
SNP_A-1997709 AA 0.004318 AA 1419.722412 285.618958
SNP_A-1997896 AB 0.004062 AB 1417.126953 1797.779175
SNP_A-1997922 AA 0.001898 AA 1317.688965 239.883804
SNP_A-2000230 AA 0.002151 AA 2401.156250 901.980286
SNP_A-2000332 AA 0.003803 AA 3109.533936 631.228516
SNP_A-2000337 AA 0.000676 AA 1616.659546 293.112244
SNP_A-2000342 AA 0.002112 AA 3178.157227 902.638245
SNP_A-4268172 AB 0.024836 AB 496.185608 1033.674438

Total number of rows: 934968

Table truncated, full table size 47496 Kbytes.




Supplementary file Size Download File type/resource
GSM917619_MT334_MDT-MB-148.CEL.gz 30.0 Mb (ftp)(http) CEL
GSM917619_MT334_MDT-MB-148.birdseed.chp.gz 13.6 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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