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Sample GSM917717 Query DataSets for GSM917717
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-310 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 5.0
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-310
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 0.004010 BB 629.445557 2039.399658
SNP_A-1967418 BB 0.001190 BB 254.671570 801.044800
SNP_A-1969580 BB 0.003751 BB 1717.766968 5413.653809
SNP_A-4263484 BB 0.001047 BB 521.429260 1706.457520
SNP_A-1978185 AA 0.007610 AA 863.712952 287.966644
SNP_A-4264431 AA 0.005882 AA 3138.849854 425.862976
SNP_A-1980898 AB 0.002238 AB 1038.792358 1002.501465
SNP_A-1983139 AA 0.014359 AA 1093.100342 462.898651
SNP_A-4265735 AB 0.003186 AB 1282.809692 1118.060791
SNP_A-1995832 AA 0.001638 AA 2166.507324 492.118561
SNP_A-1995893 AA 0.002198 AA 2446.072998 1001.155884
SNP_A-1997689 BB 0.002191 BB 735.215393 3370.793945
SNP_A-1997709 AA 0.009320 AA 2186.928467 298.235168
SNP_A-1997896 AA 0.004858 AA 2532.868408 527.228943
SNP_A-1997922 AA 0.003031 AA 1468.832886 292.356018
SNP_A-2000230 AA 0.006472 AA 2703.460693 810.881165
SNP_A-2000332 AB 0.006645 AB 2908.360107 2946.134766
SNP_A-2000337 AA 0.002232 AA 1662.642944 311.507721
SNP_A-2000342 AA 0.002083 AA 3597.624268 850.115356
SNP_A-4268172 AB 0.009337 AB 804.309204 1085.909180

Total number of rows: 934968

Table truncated, full table size 47484 Kbytes.




Supplementary file Size Download File type/resource
GSM917717_MT11_MDT-MB-310.CEL.gz 28.6 Mb (ftp)(http) CEL
GSM917717_MT11_MDT-MB-310.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

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