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Sample GSM1905475 Query DataSets for GSM1905475
Status Public on Oct 10, 2015
Title 644988_11288_2
Sample type genomic
 
Channel 1
Source name Tumor
Organism Homo sapiens
Characteristics mutation status: BRAF V600E
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 1.31E-01
2 1.64E-02
3 -5.74E-02
4 -1.36E-01
5 1.66E-01
6 -9.48E-02
7 -5.75E-02
8 2.05E-01
9 -7.35E-02
10 -2.37E-02
11 -1.47E-01
12 2.79E-01
13 -7.77E-02
14 -8.47E-02
15 -1.33E-01
16 3.61E-01
17 -2.71E-01
18 -1.76E-01
19 -1.35E-01
20 4.55E-02

Total number of rows: 420288

Table truncated, full table size 6685 Kbytes.




Supplementary file Size Download File type/resource
GSM1905475_644988_11288_2.txt.gz 121.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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