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Sample GSM1048986 Query DataSets for GSM1048986
Status Public on Dec 06, 2012
Title Uveal melanoma from enucleation 77 [RPCI]
Sample type genomic
 
Channel 1
Source name Uveal melanoma from enucleation 77
Organism Homo sapiens
Characteristics tissue: Fresh frozen sample from enucleated eye
disease: Primary uveal melanoma tumor
gep class: 1
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was prepared using the Wizard Genomic DNA purification kit (Promega).
Label Cy3
Label protocol 1μg of reference and test sample genomic DNA were individually fluorescently labeled using the BioArray CGH Labeling System following manufacturer's protocol.
 
Channel 2
Source name Normal Human Male Reference DNA
Organism Homo sapiens
Characteristics reference: Normal Human Male Reference DNA
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was prepared using the Wizard Genomic DNA purification kit (Promega).
Label Cy5
Label protocol 1μg of reference and test sample genomic DNA were individually fluorescently labeled using the BioArray CGH Labeling System following manufacturer's protocol.
 
 
Hybridization protocol DNA was hybridized to the arrays for 16 hours at 55°C using a GeneTAC hybridization station (Genomic Solutions, Inc.).
Scan protocol The hybridized aCGH slides were then scanned using a GenePix 4200A Scanner (Molecular Devices) to generate images for both Cy3 (test) and Cy5 (control) channels.
Image analysis was performed using the ImaGene (version 6.0.1) software from BioDiscovery, Inc.
Data processing A loess corrected log2 ratio of the background subtracted test/control was calculated for each clone to compensate for non-linear raw aCGH profiles in each sample.
 
Submission date Dec 05, 2012
Last update date Dec 06, 2012
Contact name Michael D Onken
Organization name Washington University School of Medicine
Department Biochemistry & Molecular Biophysics
Lab Box 8231
Street address 660 S. Euclid Ave
City Saint Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
Platform ID GPL16342
Series (2)
GSE42738 Chromosomal changes in primary human uveal melanomas [RPCI]
GSE42740 Chromosomal changes in primary human uveal melanomas

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy3/Cy5) representing test/reference

Data table
ID_REF VALUE
RP11-1005F9 0.0796
RP11-1006C22 -0.093
RP11-1007I1 0.081
RP11-1007K14 0.0457
RP11-1008O5 0.0241
RP11-1008P7 -0.0855
RP11-100A11 -0.0758
RP11-100A3 0.0244
RP11-100B11 0.0582
RP11-100B16 0.0563
RP11-100B17 -0.1306
RP11-100C21 0.1296
RP11-100C23 -0.0441
RP11-100E15 -0.2775
RP11-100E5 0.0009
RP11-100E7 -0.2588
RP11-100G15 0.0149
RP11-100H7 0.0944
RP11-100I1 0.0677
RP11-100K2

Total number of rows: 5802

Table truncated, full table size 102 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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