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Sample GSM917690 Query DataSets for GSM917690
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-210 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 12.2
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-210
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 0.004724 BB 667.867798 2052.197998
SNP_A-1967418 BB 0.000383 BB 263.953491 753.659058
SNP_A-1969580 BB 0.010189 BB 2030.966064 6064.057617
SNP_A-4263484 AA 0.002816 AA 2691.834473 371.424500
SNP_A-1978185 AA 0.001962 AA 1097.238037 312.682312
SNP_A-4264431 AA 0.003748 AA 2728.878906 307.019287
SNP_A-1980898 AB 0.002820 AB 1221.239502 1043.754150
SNP_A-1983139 AA 0.001191 AA 1511.128418 448.215912
SNP_A-4265735 AB 0.002670 AB 1168.919312 989.169250
SNP_A-1995832 BB 0.007002 BB 627.677429 2206.119385
SNP_A-1995893 BB 0.003165 BB 541.412659 2299.029785
SNP_A-1997689 BB 0.001683 BB 654.900391 2880.199463
SNP_A-1997709 AA 0.002751 AA 1511.530884 286.542603
SNP_A-1997896 AA 0.016594 AA 2909.993408 484.875671
SNP_A-1997922 BB 0.006257 BB 442.716217 1635.835693
SNP_A-2000230 AA 0.001206 AA 2420.389160 960.151489
SNP_A-2000332 AB 0.005682 AB 2939.493652 2704.170166
SNP_A-2000337 AA 0.005995 AA 1741.932007 341.048523
SNP_A-2000342 AA 0.003510 AA 3186.393799 724.907654
SNP_A-4268172 AA 0.001457 AA 700.741943 282.412354

Total number of rows: 934968

Table truncated, full table size 47487 Kbytes.




Supplementary file Size Download File type/resource
GSM917690_MT401_MDT-MB-210.CEL.gz 29.4 Mb (ftp)(http) CEL
GSM917690_MT401_MDT-MB-210.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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