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Sample GSM917715 Query DataSets for GSM917715
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-308 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 24.0
gender: M
histological subtype: Classic
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-308
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 0.004225 BB 597.264832 1984.678223
SNP_A-1967418 BB 0.002254 BB 269.224213 681.068420
SNP_A-1969580 BB 0.007891 BB 1967.097534 5401.680176
SNP_A-4263484 AB 0.005620 AB 2019.440430 1448.232788
SNP_A-1978185 AA 0.001552 AA 1129.898560 277.325348
SNP_A-4264431 AA 0.003544 AA 2981.001221 445.028625
SNP_A-1980898 AB 0.002857 AB 1246.480347 941.212402
SNP_A-1983139 AA 0.007375 AA 1064.640503 383.364807
SNP_A-4265735 BB 0.000442 BB 468.190247 1612.793213
SNP_A-1995832 AA 0.002012 AA 1851.749268 381.669647
SNP_A-1995893 AA 0.003486 AA 1983.935059 865.102051
SNP_A-1997689 BB 0.000679 BB 680.257935 3131.478760
SNP_A-1997709 AA 0.008620 AA 2142.259033 323.091675
SNP_A-1997896 AA 0.010863 AA 2783.374268 535.954956
SNP_A-1997922 AA 0.006961 AA 1565.397827 261.138184
SNP_A-2000230 AA 0.003957 AA 2825.524414 945.720764
SNP_A-2000332 AA 0.003738 AA 3657.303711 684.025452
SNP_A-2000337 AA 0.011137 AA 1817.409912 200.851883
SNP_A-2000342 AA 0.004868 AA 3107.046631 975.779114
SNP_A-4268172 AB 0.004912 AB 662.130920 1073.409668

Total number of rows: 934968

Table truncated, full table size 47492 Kbytes.




Supplementary file Size Download File type/resource
GSM917715_MT9_MDT-MB-308.CEL.gz 29.6 Mb (ftp)(http) CEL
GSM917715_MT9_MDT-MB-308.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

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