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Sample GSM917639 Query DataSets for GSM917639
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-175 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 7.0
gender: M
histological subtype: Desmoplastic
subgroup: SHH
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-175
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 0.008266 BB 530.137329 1736.243286
SNP_A-1967418 BB 0.006198 BB 300.372162 633.814941
SNP_A-1969580 BB 0.004459 BB 1017.432312 3851.342285
SNP_A-4263484 AA 0.004765 AA 2034.054199 279.119781
SNP_A-1978185 AA 0.001427 AA 1349.225830 360.390625
SNP_A-4264431 AB 0.016348 AB 1157.092651 779.099060
SNP_A-1980898 BB 0.005383 BB 279.525208 1108.642578
SNP_A-1983139 AA 0.027253 AA 1307.202759 581.811218
SNP_A-4265735 AB 0.012634 AB 584.270142 681.587646
SNP_A-1995832 AB 0.003246 AB 1565.759399 1185.105469
SNP_A-1995893 AB 0.002151 AB 1360.798950 1442.183228
SNP_A-1997689 BB 0.003681 BB 516.618774 3057.838379
SNP_A-1997709 AA 0.005585 AA 1312.284058 230.514694
SNP_A-1997896 AA 0.009339 AA 1583.305908 501.126770
SNP_A-1997922 AA 0.005358 AA 1056.627441 242.001846
SNP_A-2000230 NC 0.411168 AA 1489.005981 1142.909424
SNP_A-2000332 AB 0.000902 AB 2490.554688 2439.281982
SNP_A-2000337 AA 0.005265 AA 1383.722168 327.702209
SNP_A-2000342 AA 0.005076 AA 2896.647461 861.261292
SNP_A-4268172 AA 0.008122 AA 499.650452 232.831024

Total number of rows: 934968

Table truncated, full table size 47479 Kbytes.




Supplementary file Size Download File type/resource
GSM917639_MT367_MDT-MB-175.CEL.gz 29.4 Mb (ftp)(http) CEL
GSM917639_MT367_MDT-MB-175.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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