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Sample GSM141883 Query DataSets for GSM141883
Status Public on Oct 24, 2006
Title HF0992_Hind_3
Sample type genomic
 
Source name Brain tissue (snap-frozen sections) from glioma patient of Henry Ford Hospital
Organism Homo sapiens
Characteristics Tissue: brain tumor, Histopathological diagnosis: glioblastoma, grade 4
Biomaterial provider Hermelin Brain Tumor Center, Departments Neurology and Neurosurgery at the Henry Ford Hospital (Detroit, MI)
Extracted molecule genomic DNA
Extraction protocol Extraction of genomic DNA with high molecular weight was performed using QIamp micro DNA extraction kit (Qiagen, Valencia, CA) following the manufacturer's instructions.
Label biotin
Label protocol Standard Affymetrix procedures
 
Hybridization protocol Standard Affymetrix procedures
Scan protocol Standard Affymetrix procedures using high-resolution microarray scanner 3000, GCOS 1.2
Description Snap-frozen sections of areas immediately adjacent to the region used for the histopathologic diagnosis
Data processing DAT and CEL files were processed by Affymetrix GCOS 1.2 with default analysis settings. Calls generated by GDAS 3.0 with confidence threshold 0.25. Copy numbers were generated by Affymetrix Chromosome Copy Number Tool, which uses reference set of 145 normal individuals.
 
Submission date Oct 23, 2006
Last update date Oct 22, 2007
Contact name Howard Fine
E-mail(s) hfine@mail.nih.gov
Phone 301-402-6383
Fax 301-480-2246
Organization name National Cancer Institute
Department Neurological Disorders and Stroke
Street address 9030 Old Georgetown Rd
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL2004
Series (1)
GSE6109 High-resolution Global Genomic Survey of 178 Gliomas

Data table header descriptions
ID_REF Affymetrix probe set ID
VALUE Genotype call by dynamic model algorithm
SPA_CN Copy number by Single Point Analysis
SPA_PVAL Copy number p-value by Single Point Analysis
GSA_CN Copy number by Genome Smoothed Analysis (over 500 kb)
GSA_PVAL Copy number p-value by Genome Smoothed Analysis
LOH Loss of Heterozygosity (probability score)
LOG2RATIO Log2 ratio of probeset signal intensity in the sample to the mean in the reference set (genotype-corrected)

Data table
ID_REF VALUE SPA_CN SPA_PVAL GSA_CN GSA_PVAL LOH LOG2RATIO
SNP_A-1718890 BB 5.640810 7.224720 5.640810 7.224720 0.545785 2.322395
SNP_A-1668776 BB 4.352398 4.878367 3.444316 5.098680 0.545785 1.736044
SNP_A-1723597 AA 2.570986 0.931748 3.442366 5.157118 0.545785 0.545622
SNP_A-1728870 AB 3.731564 4.309848 3.441566 5.184596 0.000000 1.388034
SNP_A-1669946 AA 1.964131 -0.369364 3.361013 4.798490 1.709680 -0.063203
SNP_A-1708099 AA 2.854081 1.724791 3.360868 4.798852 1.709680 0.781836
SNP_A-1716798 BB 5.217696 20.000000 3.357394 4.807217 1.709680 2.146079
SNP_A-1701872 BB 2.844468 1.657454 3.181485 3.819561 1.709680 0.774207
SNP_A-1697748 NoCall 3.324219 1.082403 3.057550 1.364517 1.709680 1.126647
SNP_A-1699138 BB 2.903959 1.161989 3.057564 1.364503 1.709680 0.821013
SNP_A-1750020 BB 3.145190 1.574523 3.059295 1.362778 1.709680 1.001461
SNP_A-1646481 BB 1.997300 -0.330671 1.997300 -0.330671 1.709680 -0.025335
SNP_A-1701882 AB 2.197712 0.632282 2.435501 0.900686 0.000000 0.190890
SNP_A-1701982 AB 3.030255 2.353825 2.435499 0.900676 0.000000 0.917280
SNP_A-1749896 AA 1.936710 -0.367657 2.434632 0.892373 2.002868 -0.094995
SNP_A-1750090 BB 2.131211 0.438302 2.434628 0.892331 2.002868 0.121408
SNP_A-1714480 BB 2.889490 1.437735 2.344097 0.666542 2.002868 0.809718
SNP_A-1649717 AA 1.858107 -0.525469 1.826209 -0.680928 2.002868 -0.188685
SNP_A-1703834 BB 1.652057 -1.011734 1.517091 -1.429538 2.002868 -0.454469
SNP_A-1695724 BB 1.738653 -0.476271 2.155783 0.422000 2.002868 -0.338941

Total number of rows: 57244

Table truncated, full table size 4062 Kbytes.




Supplementary data files not provided

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