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Sample GSM917339 Query DataSets for GSM917339
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-52 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 10.0
gender: F
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-52
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 0.003161 BB 679.332275 2903.090576
SNP_A-1967418 BB 0.001816 BB 245.583298 805.219543
SNP_A-1969580 BB 0.003835 BB 1615.169556 4663.135742
SNP_A-4263484 AB 0.006069 AB 1815.826538 1453.426514
SNP_A-1978185 AA 0.003759 AA 1001.693970 296.269257
SNP_A-4264431 AA 0.001550 AA 2426.790283 330.385406
SNP_A-1980898 AB 0.002836 AB 895.080505 864.817444
SNP_A-1983139 AA 0.002193 AA 1926.570679 558.222656
SNP_A-4265735 AA 0.003610 AA 1878.425903 392.791504
SNP_A-1995832 AA 0.001111 AA 1918.952637 406.098816
SNP_A-1995893 AA 0.000548 AA 2248.113770 965.121521
SNP_A-1997689 BB 0.000939 BB 691.469116 3139.285889
SNP_A-1997709 AA 0.007464 AA 2109.942871 315.926300
SNP_A-1997896 AA 0.001608 AA 2157.853271 559.036926
SNP_A-1997922 AA 0.001611 AA 1280.552979 323.503571
SNP_A-2000230 AA 0.002568 AA 2809.697998 1017.443176
SNP_A-2000332 AA 0.007191 AA 4052.612549 920.155945
SNP_A-2000337 AA 0.004032 AA 1853.706055 270.456757
SNP_A-2000342 AA 0.004716 AA 3433.900879 1046.804077
SNP_A-4268172 AA 0.000348 AA 751.679504 279.689301

Total number of rows: 934968

Table truncated, full table size 47501 Kbytes.




Supplementary file Size Download File type/resource
GSM917339_MT673_MDT-MB-52.CEL.gz 30.0 Mb (ftp)(http) CEL
GSM917339_MT673_MDT-MB-52.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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