NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM917330 Query DataSets for GSM917330
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-41 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 9.0
gender: M
histological subtype: Desmoplastic
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-41
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 0.003994 AB 1571.417480 1265.333862
SNP_A-1967418 BB 0.005218 BB 328.499298 729.850525
SNP_A-1969580 BB 0.003840 BB 1636.936646 4719.754395
SNP_A-4263484 AB 0.004192 AB 1660.043457 933.316101
SNP_A-1978185 AA 0.002338 AA 1095.213867 252.503540
SNP_A-4264431 AA 0.003443 AA 2674.664062 302.288300
SNP_A-1980898 AB 0.007133 AB 1199.874756 1208.136841
SNP_A-1983139 AA 0.001486 AA 1700.865723 448.233398
SNP_A-4265735 BB 0.016991 BB 441.467621 2109.793457
SNP_A-1995832 AB 0.011176 AB 1647.990234 1583.803955
SNP_A-1995893 AB 0.001613 AB 1417.964722 1475.015991
SNP_A-1997689 BB 0.005991 BB 558.243896 2404.030762
SNP_A-1997709 AA 0.011919 AA 1490.174683 338.548553
SNP_A-1997896 AA 0.002940 AA 2410.431641 507.787659
SNP_A-1997922 AB 0.007785 AB 726.839783 927.424255
SNP_A-2000230 AA 0.002138 AA 2361.545410 1050.128906
SNP_A-2000332 AA 0.009420 AA 4161.812988 953.567261
SNP_A-2000337 AA 0.015732 AA 1616.591431 393.726624
SNP_A-2000342 AA 0.005001 AA 2901.107666 743.413330
SNP_A-4268172 AA 0.003067 AA 838.601013 234.874649

Total number of rows: 934968

Table truncated, full table size 47492 Kbytes.




Supplementary file Size Download File type/resource
GSM917330_MT664_MDT-MB-41.CEL.gz 28.5 Mb (ftp)(http) CEL
GSM917330_MT664_MDT-MB-41.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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap