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Sample GSM917635 Query DataSets for GSM917635
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-169 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 9.0
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-169
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 0.014998 BB 838.092224 3664.180176
SNP_A-1967418 AB 0.009958 AB 427.194153 459.692749
SNP_A-1969580 BB 0.003915 BB 1141.100464 3908.491699
SNP_A-4263484 BB 0.003662 BB 396.582947 1477.607544
SNP_A-1978185 AA 0.002706 AA 1403.891479 319.264008
SNP_A-4264431 AB 0.009574 AB 1225.772827 932.477600
SNP_A-1980898 AA 0.091228 AA 1053.769043 252.246918
SNP_A-1983139 AA 0.013545 AA 1029.194214 428.392242
SNP_A-4265735 AA 0.002379 AA 1869.166016 481.619629
SNP_A-1995832 AA 0.015594 AA 2694.524902 630.031433
SNP_A-1995893 AA 0.007923 AA 2722.646729 1113.527588
SNP_A-1997689 BB 0.005311 BB 774.086182 2899.656738
SNP_A-1997709 AA 0.009341 AA 2172.644043 286.792419
SNP_A-1997896 AA 0.010638 AA 1557.096069 519.692749
SNP_A-1997922 AA 0.004106 AA 1097.894409 251.218964
SNP_A-2000230 AA 0.017338 AA 2358.785645 1392.501709
SNP_A-2000332 BB 0.017362 BB 1623.415894 4660.255371
SNP_A-2000337 AA 0.067704 AA 1028.932251 470.611664
SNP_A-2000342 AA 0.006849 AA 2755.253418 778.360657
SNP_A-4268172 AA 0.003750 AA 606.788330 244.147873

Total number of rows: 934968

Table truncated, full table size 47467 Kbytes.




Supplementary file Size Download File type/resource
GSM917635_MT362_MDT-MB-169.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM917635_MT362_MDT-MB-169.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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