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Sample GSM917630 Query DataSets for GSM917630
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-163 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 2.0
gender: M
histological subtype: Classic
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-163
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 0.005262 AB 1892.196899 2116.049316
SNP_A-1967418 BB 0.014579 BB 148.803665 542.570862
SNP_A-1969580 BB 0.001370 BB 1266.713501 4569.377441
SNP_A-4263484 AA 0.018170 AA 1705.259399 360.911011
SNP_A-1978185 AA 0.000772 AA 1224.433350 292.977325
SNP_A-4264431 AA 0.020414 AA 1486.470825 280.429596
SNP_A-1980898 BB 0.003970 BB 219.471466 1180.806396
SNP_A-1983139 AA 0.003011 AA 1427.052002 485.551239
SNP_A-4265735 AA 0.006050 AA 1236.368286 349.450897
SNP_A-1995832 BB 0.002437 BB 481.233734 1873.847778
SNP_A-1995893 BB 0.004722 BB 297.170288 2125.444336
SNP_A-1997689 BB 0.001339 BB 588.716248 3083.123779
SNP_A-1997709 AA 0.001394 AA 1640.115845 288.780579
SNP_A-1997896 AA 0.001333 AA 2003.469116 489.838593
SNP_A-1997922 BB 0.004110 BB 423.906555 1279.866211
SNP_A-2000230 AA 0.017648 AA 1682.276245 677.694702
SNP_A-2000332 BB 0.004390 BB 1029.375122 3974.316162
SNP_A-2000337 AA 0.008134 AA 1170.221069 262.452728
SNP_A-2000342 AA 0.010341 AA 2587.286377 720.992188
SNP_A-4268172 AA 0.008482 AA 500.587097 251.415009

Total number of rows: 934968

Table truncated, full table size 47475 Kbytes.




Supplementary file Size Download File type/resource
GSM917630_MT356_MDT-MB-163.CEL.gz 28.8 Mb (ftp)(http) CEL
GSM917630_MT356_MDT-MB-163.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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