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Sample GSM917396 Query DataSets for GSM917396
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-112 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 8.0
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-112
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 0.009473 BB 506.012573 1677.406250
SNP_A-1967418 BB 0.001007 BB 287.416870 768.881714
SNP_A-1969580 BB 0.004869 BB 1269.341064 3943.198975
SNP_A-4263484 AB 0.018977 AB 801.857178 745.174500
SNP_A-1978185 AA 0.005770 AA 913.569702 256.943237
SNP_A-4264431 AB 0.001478 AB 1677.487549 1376.250122
SNP_A-1980898 BB 0.000603 BB 290.275482 1407.611938
SNP_A-1983139 AA 0.006436 AA 1357.575928 313.387299
SNP_A-4265735 AB 0.004429 AB 849.973206 833.946167
SNP_A-1995832 BB 0.006371 BB 360.333344 1385.853516
SNP_A-1995893 BB 0.008435 BB 385.078979 1699.536133
SNP_A-1997689 BB 0.004962 BB 680.793213 2617.579102
SNP_A-1997709 AA 0.016183 AA 977.134827 255.169083
SNP_A-1997896 BB 0.009303 BB 543.480957 2598.151611
SNP_A-1997922 AA 0.006234 AA 1147.079590 170.188400
SNP_A-2000230 AA 0.003005 AA 2555.400635 874.578918
SNP_A-2000332 BB 0.002088 BB 1061.925415 3536.412598
SNP_A-2000337 AA 0.004846 AA 1512.729858 229.431671
SNP_A-2000342 AA 0.005611 AA 3908.848389 1003.971619
SNP_A-4268172 AA 0.001681 AA 839.691284 269.604187

Total number of rows: 934968

Table truncated, full table size 47485 Kbytes.




Supplementary file Size Download File type/resource
GSM917396_MT293_MDT-MB-112.CEL.gz 28.6 Mb (ftp)(http) CEL
GSM917396_MT293_MDT-MB-112.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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