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Sample GSM917725 Query DataSets for GSM917725
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-320 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 2.0
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-320
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 0.006334 BB 669.445312 1977.990967
SNP_A-1967418 AB 0.057488 AB 715.038086 473.953278
SNP_A-1969580 BB 0.005331 BB 1487.279907 5378.303711
SNP_A-4263484 AB 0.000826 AB 1720.778076 1117.549927
SNP_A-1978185 AA 0.003271 AA 1050.581665 232.212601
SNP_A-4264431 AA 0.001421 AA 2759.871582 381.621735
SNP_A-1980898 BB 0.003926 BB 325.908752 1763.135986
SNP_A-1983139 AA 0.006153 AA 1107.865234 373.654724
SNP_A-4265735 AA 0.004461 AA 1820.586426 556.441589
SNP_A-1995832 BB 0.002321 BB 625.309937 1821.540771
SNP_A-1995893 BB 0.001926 BB 378.635803 2018.968506
SNP_A-1997689 BB 0.001367 BB 704.660706 3300.015869
SNP_A-1997709 AA 0.000824 AA 1579.296997 267.003937
SNP_A-1997896 AB 0.005209 AB 1589.058960 2561.191406
SNP_A-1997922 AB 0.001015 AB 934.849304 960.238647
SNP_A-2000230 AA 0.003964 AA 2914.661621 1025.537354
SNP_A-2000332 AA 0.005093 AA 3148.390625 561.435852
SNP_A-2000337 AA 0.008629 AA 1502.961914 360.785583
SNP_A-2000342 AA 0.002549 AA 3096.873535 874.324341
SNP_A-4268172 AB 0.012372 AB 833.184204 1169.563477

Total number of rows: 934968

Table truncated, full table size 47497 Kbytes.




Supplementary file Size Download File type/resource
GSM917725_MT21_MDT-MB-320.CEL.gz 29.6 Mb (ftp)(http) CEL
GSM917725_MT21_MDT-MB-320.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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