NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1905456 Query DataSets for GSM1905456
Status Public on Oct 10, 2015
Title 630758_17203_2
Sample type genomic
 
Channel 1
Source name Tumor
Organism Homo sapiens
Characteristics mutation status: NRAS Q61L
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 -3.60E-02
2 -7.79E-02
3 -3.30E-01
4 -2.66E-02
5 -1.73E-01
6 8.45E-03
7 -4.75E-02
8 4.32E-02
9 5.64E-02
10 7.40E-02
11 3.53E-01
12 -3.57E-03
13 2.08E-01
14 1.40E-01
15 -1.15E-01
16 -8.93E-02
17 -4.33E-01
18 -7.17E-02
19 -3.37E-02
20 -2.71E-02

Total number of rows: 420288

Table truncated, full table size 6668 Kbytes.




Supplementary file Size Download File type/resource
GSM1905456_630758_17203_2.txt.gz 43.6 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap