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Sample GSM1905435 Query DataSets for GSM1905435
Status Public on Oct 10, 2015
Title 624080_11287_1
Sample type genomic
 
Channel 1
Source name Tumor
Organism Homo sapiens
Characteristics mutation status: WT
tissue: melanoma
Treatment protocol N/A
Growth protocol N/A
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using sodium thiocyanate as described in Wilson et al. Clinical Cancer Research 20(12):3328-37, 2014.
Label Cy5
Label protocol Tumor DNA was labeled using BioPrime® Array CGH Genomic Labeling System (Life Technologies, Grand Island, NY) according to manufacturer’s instructions
 
Channel 2
Source name Pooled Normal
Organism Homo sapiens
Characteristics gender: Female
sample type: reference
Treatment protocol N/A
Growth protocol N/A
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using sodium thiocyanate as described in Wilson et al. Clinical Cancer Research 20(12):3328-37, 2014.
Label Cy3
Label protocol Tumor DNA was labeled using BioPrime® Array CGH Genomic Labeling System (Life Technologies, Grand Island, NY) according to manufacturer’s instructions
 
 
Hybridization protocol Array-based comparative genomic hybridization (aCGH) was performed using the Agilent SurePrint G3 Human CGH 2x400K M microarrays following manufacturer’s instructions
Scan protocol Scanned on Agilent scanner
Data processing Images were quantified using Agilent Feature Extraction Software and extracted data were analyzed using BioDiscovery’s Nexus 7 copy-number software (Nexus Genomics Inc.)
 
Submission date Oct 09, 2015
Last update date Oct 10, 2015
Contact name Katherine Nathanson
E-mail(s) knathans@exchange.upenn.edu
Organization name Perelman School of Medicine at the University of Pennsylvania
Street address 421 Curie Blvd
City Philadelphia
State/province PA
ZIP/Postal code 19103
Country USA
 
Platform ID GPL9777
Series (1)
GSE73899 Copy number analysis in melanoma tumor samples from E2603

Data table header descriptions
ID_REF
VALUE Lowess-normalized log10 ratios in the FE files (Cy5/Cy3) representing test/reference (control)

Data table
ID_REF VALUE
1 1.37E-01
2 1.26E-01
3 9.28E-02
4 -1.79E-01
5 2.37E-01
6 -1.08E-02
7 -4.85E-02
8 1.39E-01
9 -6.18E-02
10 -9.72E-02
11 -4.12E-02
12 2.99E-01
13 -3.56E-02
14 -8.75E-02
15 3.36E-02
16 2.68E-01
17 -3.31E-01
18 5.95E-02
19 -7.90E-02
20 2.01E-01

Total number of rows: 420288

Table truncated, full table size 6688 Kbytes.




Supplementary file Size Download File type/resource
GSM1905435_624080_11287_1.txt.gz 121.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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