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Sample GSM917693 Query DataSets for GSM917693
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-213 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 2.0
gender: M
histological subtype: Desmoplastic
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-213
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 0.000130 BB 600.687744 2468.094727
SNP_A-1967418 AB 0.001847 AB 635.623291 579.590881
SNP_A-1969580 BB 0.009682 BB 1310.437988 5343.629395
SNP_A-4263484 BB 0.001897 BB 469.383392 1867.634766
SNP_A-1978185 AA 0.004137 AA 986.953613 298.838470
SNP_A-4264431 AA 0.008928 AA 3109.296143 328.596924
SNP_A-1980898 AB 0.000730 AB 1020.215759 901.690735
SNP_A-1983139 AA 0.001492 AA 1751.687622 538.858948
SNP_A-4265735 AB 0.002734 AB 1036.494385 904.541626
SNP_A-1995832 AB 0.001900 AB 1273.609375 1009.352722
SNP_A-1995893 AB 0.003534 AB 1669.407837 1678.698853
SNP_A-1997689 BB 0.000813 BB 670.642090 3043.485107
SNP_A-1997709 AA 0.000250 AA 1635.555908 271.439636
SNP_A-1997896 AB 0.003415 AB 1405.488403 2367.992188
SNP_A-1997922 AA 0.001550 AA 1321.873779 328.596924
SNP_A-2000230 AA 0.002321 AA 2375.120850 898.007019
SNP_A-2000332 AA 0.011830 AA 4230.450684 811.688538
SNP_A-2000337 AA 0.001971 AA 1737.235352 294.083099
SNP_A-2000342 AA 0.006887 AA 3780.361328 763.172546
SNP_A-4268172 AA 0.001002 AA 829.854187 296.720306

Total number of rows: 934968

Table truncated, full table size 47482 Kbytes.




Supplementary file Size Download File type/resource
GSM917693_MT404_MDT-MB-213.CEL.gz 29.5 Mb (ftp)(http) CEL
GSM917693_MT404_MDT-MB-213.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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