NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM917629 Query DataSets for GSM917629
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-162 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 5.0
gender: F
histological subtype: Desmoplastic
subgroup: Group 4
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-162
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 0.000853 AB 1621.333252 1530.288208
SNP_A-1967418 BB 0.006762 BB 239.701416 562.710205
SNP_A-1969580 BB 0.001137 BB 1260.798828 4423.962402
SNP_A-4263484 AB 0.011406 AB 1092.085083 687.342468
SNP_A-1978185 AA 0.001122 AA 1320.072388 324.493347
SNP_A-4264431 AA 0.015117 AA 1645.906006 303.123505
SNP_A-1980898 AB 0.011252 AB 649.138062 584.439575
SNP_A-1983139 AA 0.005420 AA 1164.635376 350.027283
SNP_A-4265735 AB 0.013091 AB 601.907410 637.823669
SNP_A-1995832 AA 0.002830 AA 2222.895508 434.407166
SNP_A-1995893 AA 0.004270 AA 2289.957031 771.646484
SNP_A-1997689 BB 0.002515 BB 543.233154 2970.810791
SNP_A-1997709 AA 0.000623 AA 1717.473267 280.908356
SNP_A-1997896 AA 0.003101 AA 1853.664551 467.664551
SNP_A-1997922 AA 0.009123 AA 968.389099 275.101654
SNP_A-2000230 AA 0.017563 AA 1656.057617 961.746033
SNP_A-2000332 AB 0.007310 AB 2116.113525 2064.023926
SNP_A-2000337 AA 0.006825 AA 1438.831055 346.048859
SNP_A-2000342 AA 0.008883 AA 2687.620605 689.415344
SNP_A-4268172 AA 0.013030 AA 433.932617 244.423615

Total number of rows: 934968

Table truncated, full table size 47475 Kbytes.




Supplementary file Size Download File type/resource
GSM917629_MT355_MDT-MB-162.CEL.gz 29.6 Mb (ftp)(http) CEL
GSM917629_MT355_MDT-MB-162.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

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