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Sample GSM917615 Query DataSets for GSM917615
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-144 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 10.0
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-144
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 0.005375 BB 739.916748 3115.105225
SNP_A-1967418 BB 0.005008 BB 290.184723 947.390930
SNP_A-1969580 BB 0.003644 BB 1623.168335 5383.195801
SNP_A-4263484 BB 0.004917 BB 445.592133 1428.619263
SNP_A-1978185 AA 0.000639 AA 1275.828369 353.059357
SNP_A-4264431 AB 0.007944 AB 2103.594238 1578.302612
SNP_A-1980898 BB 0.001253 BB 310.836700 1372.077637
SNP_A-1983139 AA 0.005688 AA 1965.458496 445.592133
SNP_A-4265735 BB 0.003307 BB 537.621033 1811.989624
SNP_A-1995832 BB 0.001433 BB 502.745422 1838.162476
SNP_A-1995893 BB 0.004980 BB 553.202454 2508.591797
SNP_A-1997689 BB 0.002867 BB 677.396301 3527.104980
SNP_A-1997709 AA 0.006351 AA 1459.033691 308.141052
SNP_A-1997896 AB 0.003912 AB 1619.624634 2484.889160
SNP_A-1997922 AB 0.003066 AB 811.294006 898.362549
SNP_A-2000230 AA 0.004782 AA 2960.083496 1173.518311
SNP_A-2000332 AA 0.009382 AA 3953.757324 637.848877
SNP_A-2000337 AA 0.005919 AA 1605.115967 345.961090
SNP_A-2000342 AA 0.003392 AA 3765.894287 946.091248
SNP_A-4268172 AA 0.005022 AA 598.370361 293.130768

Total number of rows: 934968

Table truncated, full table size 47480 Kbytes.




Supplementary file Size Download File type/resource
GSM917615_MT330_MDT-MB-144.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM917615_MT330_MDT-MB-144.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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