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Sample GSM917703 Query DataSets for GSM917703
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-225 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 1.0
gender: M
histological subtype: Desmoplastic
subgroup: SHH
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-225
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 AA 0.001961 AA 2138.282959 514.554321
SNP_A-1967418 BB 0.002368 BB 236.768875 801.740906
SNP_A-1969580 BB 0.014720 BB 1607.510254 6024.895508
SNP_A-4263484 AA 0.001347 AA 2492.915771 337.623047
SNP_A-1978185 AA 0.005101 AA 939.097656 259.678711
SNP_A-4264431 BB 0.000121 BB 537.516602 1975.481812
SNP_A-1980898 AB 0.003647 AB 1237.274048 1084.345337
SNP_A-1983139 AA 0.007403 AA 1425.563232 555.374207
SNP_A-4265735 AB 0.003318 AB 888.067871 880.943970
SNP_A-1995832 AB 0.000785 AB 1427.812744 1174.422974
SNP_A-1995893 AB 0.003991 AB 1390.089478 1779.030151
SNP_A-1997689 BB 0.002975 BB 648.859253 2727.761475
SNP_A-1997709 AA 0.000742 AA 1608.425781 276.568451
SNP_A-1997896 AA 0.012632 AA 2828.880615 517.940979
SNP_A-1997922 AB 0.000988 AB 939.097656 960.792358
SNP_A-2000230 AA 0.001352 AA 2388.381836 998.459656
SNP_A-2000332 AA 0.018819 AA 4462.438477 834.293945
SNP_A-2000337 AA 0.002566 AA 1497.759766 313.185333
SNP_A-2000342 AA 0.000717 AA 3341.862061 899.691162
SNP_A-4268172 AB 0.002680 AB 576.420654 802.973511

Total number of rows: 934968

Table truncated, full table size 47479 Kbytes.




Supplementary file Size Download File type/resource
GSM917703_MT415_MDT-MB-225.CEL.gz 29.7 Mb (ftp)(http) CEL
GSM917703_MT415_MDT-MB-225.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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