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Sample GSM1905417 Query DataSets for GSM1905417
Status Public on Oct 10, 2015
Title 617405_13612_2
Sample type genomic
 
Channel 1
Source name Tumor
Organism Homo sapiens
Characteristics mutation status: NRAS G13R
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 1.34E-01
2 0.00E+00
3 0.00E+00
4 -3.73E-02
5 -1.30E-01
6 1.24E-01
7 1.03E-01
8 1.13E-01
9 -8.35E-03
10 -9.80E-02
11 1.82E-01
12 -1.34E-01
13 5.33E-02
14 2.25E-01
15 -8.41E-02
16 -2.02E-02
17 -3.69E-04
18 3.57E-01
19 -1.28E-01
20 4.58E-01

Total number of rows: 420288

Table truncated, full table size 6667 Kbytes.




Supplementary file Size Download File type/resource
GSM1905417_617405_13612_2.txt.gz 118.9 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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