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Sample GSM917682 Query DataSets for GSM917682
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-201 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 23.0
gender: M
histological subtype: Classic
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-201
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 0.000990 BB 654.220642 2397.611816
SNP_A-1967418 BB 0.004516 BB 263.248413 616.645142
SNP_A-1969580 BB 0.001838 BB 1602.925415 5063.463867
SNP_A-4263484 BB 0.001725 BB 468.019928 1852.769043
SNP_A-1978185 AA 0.012682 AA 1707.584473 325.477905
SNP_A-4264431 AA 0.021500 AA 1472.859985 295.831787
SNP_A-1980898 BB 0.006192 BB 324.647797 1135.622925
SNP_A-1983139 AA 0.001288 AA 1550.831421 485.321259
SNP_A-4265735 AA 0.017638 AA 1022.617615 358.845886
SNP_A-1995832 AB 0.000394 AB 1341.556885 1145.716797
SNP_A-1995893 AB 0.001689 AB 1554.750488 1711.915649
SNP_A-1997689 BB 0.002179 BB 691.446655 3454.615723
SNP_A-1997709 AA 0.006329 AA 2058.801758 280.823120
SNP_A-1997896 AA 0.007121 AA 1972.046387 663.387756
SNP_A-1997922 AB 0.007231 AB 704.249023 811.969482
SNP_A-2000230 AA 0.011593 AA 1792.022339 893.846252
SNP_A-2000332 AB 0.008031 AB 2059.729492 2065.237061
SNP_A-2000337 AA 0.001116 AA 1679.195190 290.603241
SNP_A-2000342 AA 0.004469 AA 3188.535156 991.779236
SNP_A-4268172 AB 0.011662 AB 358.697968 576.062500

Total number of rows: 934968

Table truncated, full table size 47482 Kbytes.




Supplementary file Size Download File type/resource
GSM917682_MT393_MDT-MB-201.CEL.gz 30.1 Mb (ftp)(http) CEL
GSM917682_MT393_MDT-MB-201.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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