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Sample GSM917309 Query DataSets for GSM917309
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-15 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 3.0
gender: F
histological subtype: Classic
subgroup: WNT
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-15
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 0.014187 AA 1527.513672 377.722961
SNP_A-1967418 BB 0.008983 BB 370.340485 843.853149
SNP_A-1969580 BB 0.014659 BB 2054.291992 5110.535156
SNP_A-4263484 BB 0.005195 BB 424.950989 1404.833984
SNP_A-1978185 AA 0.004786 AA 954.445557 244.615982
SNP_A-4264431 AA 0.003038 AA 2801.014160 341.246368
SNP_A-1980898 BB 0.006016 BB 304.759186 1830.122314
SNP_A-1983139 AA 0.003503 AA 1835.226074 441.770630
SNP_A-4265735 AB 0.001548 AB 959.493103 984.448975
SNP_A-1995832 AB 0.018983 AB 1964.761841 1430.506958
SNP_A-1995893 AB 0.012849 AB 1454.917603 1159.328979
SNP_A-1997689 BB 0.008284 BB 497.355011 2265.091797
SNP_A-1997709 AA 0.004200 AA 1366.500000 268.936035
SNP_A-1997896 AA 0.001674 AA 2274.898926 551.640076
SNP_A-1997922 AB 0.012338 AB 639.659363 697.715393
SNP_A-2000230 AA 0.009944 AA 1935.121094 749.518982
SNP_A-2000332 AA 0.005802 AA 3599.726807 582.482361
SNP_A-2000337 AA 0.000837 AA 1549.844238 294.183624
SNP_A-2000342 AA 0.002723 AA 3053.607422 819.166016
SNP_A-4268172 BB 0.009532 BB 341.398163 1261.857910

Total number of rows: 934968

Table truncated, full table size 47498 Kbytes.




Supplementary file Size Download File type/resource
GSM917309_MT642_MDT-MB-15.CEL.gz 30.2 Mb (ftp)(http) CEL
GSM917309_MT642_MDT-MB-15.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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