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Sample GSM917642 Query DataSets for GSM917642
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-178 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 6.0
gender: F
histological subtype: Classic
subgroup: WNT
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-178
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 0.002102 BB 687.018127 2316.798584
SNP_A-1967418 BB 0.010130 BB 201.663055 518.040833
SNP_A-1969580 BB 0.013433 BB 1658.184937 6039.762695
SNP_A-4263484 AB 0.004449 AB 1401.858276 1162.672607
SNP_A-1978185 AA 0.004932 AA 947.751465 276.861694
SNP_A-4264431 AB 0.011628 AB 1134.824463 920.851624
SNP_A-1980898 BB 0.008367 BB 237.204971 970.881653
SNP_A-1983139 AA 0.004018 AA 1259.136963 374.684845
SNP_A-4265735 AA 0.007648 AA 1391.933105 494.151703
SNP_A-1995832 AB 0.005741 AB 1535.036133 1440.158936
SNP_A-1995893 AB 0.003481 AB 1546.186646 1462.485229
SNP_A-1997689 BB 0.000389 BB 657.374146 3071.468994
SNP_A-1997709 AA 0.005419 AA 1517.767578 218.254471
SNP_A-1997896 AA 0.005725 AA 1850.891968 584.784668
SNP_A-1997922 AB 0.008183 AB 728.778687 705.968506
SNP_A-2000230 AA 0.016756 AA 1683.733398 706.062561
SNP_A-2000332 AA 0.002959 AA 3693.575439 750.427002
SNP_A-2000337 AA 0.003460 AA 1424.162964 314.364929
SNP_A-2000342 AA 0.005218 AA 3049.125000 684.327454
SNP_A-4268172 AA 0.010017 AA 572.330872 341.882141

Total number of rows: 934968

Table truncated, full table size 47479 Kbytes.




Supplementary file Size Download File type/resource
GSM917642_MT370_MDT-MB-178.CEL.gz 28.7 Mb (ftp)(http) CEL
GSM917642_MT370_MDT-MB-178.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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