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Sample GSM917612 Query DataSets for GSM917612
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-140 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 12.0
gender: M
histological subtype: Classic
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-140
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 0.001441 BB 544.374756 2209.509521
SNP_A-1967418 BB 0.004414 BB 218.734299 823.968689
SNP_A-1969580 BB 0.010831 BB 2016.996094 6140.598145
SNP_A-4263484 AB 0.015448 AB 978.809692 1033.181152
SNP_A-1978185 AA 0.002558 AA 1159.328003 232.283386
SNP_A-4264431 AA 0.009546 AA 3206.672363 563.765259
SNP_A-1980898 BB 0.004488 BB 339.661530 1800.862183
SNP_A-1983139 AA 0.002350 AA 1510.242798 500.831299
SNP_A-4265735 AA 0.007360 AA 2146.253418 517.292786
SNP_A-1995832 BB 0.004178 BB 457.985748 1937.376709
SNP_A-1995893 BB 0.002676 BB 521.835754 2358.560791
SNP_A-1997689 BB 0.002629 BB 742.244690 3092.316895
SNP_A-1997709 AA 0.003713 AA 1951.512451 288.666046
SNP_A-1997896 BB 0.010138 BB 920.610413 4076.376221
SNP_A-1997922 AA 0.001345 AA 1390.732666 290.221161
SNP_A-2000230 AA 0.006257 AA 2932.536865 924.125061
SNP_A-2000332 AA 0.013234 AA 4194.153320 702.260254
SNP_A-2000337 AA 0.004090 AA 1811.870239 254.366394
SNP_A-2000342 AA 0.002162 AA 3498.684082 974.005310
SNP_A-4268172 AA 0.002262 AA 803.904480 345.340790

Total number of rows: 934968

Table truncated, full table size 47489 Kbytes.




Supplementary file Size Download File type/resource
GSM917612_MT327_MDT-MB-140.CEL.gz 29.9 Mb (ftp)(http) CEL
GSM917612_MT327_MDT-MB-140.birdseed.chp.gz 13.6 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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