NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM917632 Query DataSets for GSM917632
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-165 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 15.0
gender: F
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-165
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 0.001645 BB 719.643188 2622.645996
SNP_A-1967418 BB 0.004933 BB 255.278427 603.076599
SNP_A-1969580 BB 0.003362 BB 1291.285767 4101.478027
SNP_A-4263484 AB 0.006310 AB 1207.366821 968.049500
SNP_A-1978185 AA 0.006754 AA 1330.132568 183.931061
SNP_A-4264431 AA 0.015722 AA 1698.416016 362.271729
SNP_A-1980898 BB 0.004281 BB 249.788544 1143.959839
SNP_A-1983139 AA 0.027468 AA 1091.883301 490.969604
SNP_A-4265735 AA 0.073510 AA 875.602722 353.490875
SNP_A-1995832 BB 0.006845 BB 515.084229 2140.218750
SNP_A-1995893 BB 0.003745 BB 555.646118 2329.152832
SNP_A-1997689 BB 0.001531 BB 715.244873 3287.068359
SNP_A-1997709 AA 0.001565 AA 1516.218140 264.879700
SNP_A-1997896 AA 0.001730 AA 2188.132324 565.555847
SNP_A-1997922 BB 0.006591 BB 534.132690 1206.230225
SNP_A-2000230 AA 0.025233 AA 1434.813232 752.158142
SNP_A-2000332 AA 0.010672 AA 3665.274658 1219.161987
SNP_A-2000337 AA 0.005596 AA 1247.615112 282.916901
SNP_A-2000342 AA 0.005266 AA 3032.836182 957.366211
SNP_A-4268172 AA 0.011053 AA 475.782684 269.333557

Total number of rows: 934968

Table truncated, full table size 47477 Kbytes.




Supplementary file Size Download File type/resource
GSM917632_MT358_MDT-MB-165.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM917632_MT358_MDT-MB-165.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