NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM917716 Query DataSets for GSM917716
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-309 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 7.0
gender: M
histological subtype: Large Cell/Anaplastic
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-309
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 0.003444 AA 2000.477173 495.136902
SNP_A-1967418 BB 0.003533 BB 215.175125 747.810242
SNP_A-1969580 BB 0.039632 BB 2535.926025 5686.092285
SNP_A-4263484 AB 0.002531 AB 1914.773193 1266.525635
SNP_A-1978185 AA 0.001621 AA 1119.769531 281.180756
SNP_A-4264431 AA 0.005213 AA 3104.669434 459.897522
SNP_A-1980898 BB 0.003153 BB 322.992584 1720.008423
SNP_A-1983139 AA 0.006837 AA 1143.489624 309.592865
SNP_A-4265735 AB 0.001682 AB 1077.657471 969.671082
SNP_A-1995832 AB 0.000203 AB 1379.648071 1153.440674
SNP_A-1995893 AB 0.011756 AB 1365.662598 1130.949829
SNP_A-1997689 BB 0.005067 BB 626.647766 2515.468018
SNP_A-1997709 AA 0.005433 AA 1635.936279 320.723602
SNP_A-1997896 AA 0.007235 AA 2628.955078 624.936829
SNP_A-1997922 AB 0.002483 AB 1049.859863 901.854797
SNP_A-2000230 AB 0.004439 AB 2006.100342 2031.588379
SNP_A-2000332 AB 0.001449 AB 2626.802002 2675.255859
SNP_A-2000337 AA 0.000074 AA 1589.125854 284.304718
SNP_A-2000342 AA 0.003796 AA 2967.915527 838.020203
SNP_A-4268172 AB 0.021873 AB 912.798401 1285.040771

Total number of rows: 934968

Table truncated, full table size 47490 Kbytes.




Supplementary file Size Download File type/resource
GSM917716_MT10_MDT-MB-309.CEL.gz 28.1 Mb (ftp)(http) CEL
GSM917716_MT10_MDT-MB-309.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