NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3395631 Query DataSets for GSM3395631
Status Public on Nov 28, 2018
Title RJ279_PMT2_aCGH
Sample type genomic
 
Channel 1
Source name mammary tumor (IGF-IR induced)
Organism Mus musculus
Characteristics tissue: primary mammary tumor
strain: FVB (MTB-IGFIR transgenic mouse)
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from snap frozen tissue pieces using the Qiagen DNAeasy kit
Label Cy5
Label protocol DNA was prepared for array hybridisation using the Agilent Genomic DNA Enzymatic Labeling kit and labelled with Cy-5. Cy3-labelled genomic DNA extracted from mouse spleen was used as a common reference.
 
Channel 2
Source name Normal splenic DNA (reference)
Organism Mus musculus
Characteristics tissue: spleen
strain: C57Bl/6
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from snap frozen tissue pieces using the Qiagen DNAeasy kit
Label Cy3
Label protocol DNA was prepared for array hybridisation using the Agilent Genomic DNA Enzymatic Labeling kit and labelled with Cy-5. Cy3-labelled genomic DNA extracted from mouse spleen was used as a common reference.
 
 
Hybridization protocol 2ug of sample and reference DNA were hybridised to Agilent 244K whole mouse genome CGH arrays (Agilent, G4415A). Samples were prepared using the direct method with hybridizization and microarray washing carried out according to the manufacturer’s protocol.
Scan protocol Scanned on an Agilent G2505C scanner
Data processing Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.
 
Submission date Sep 19, 2018
Last update date Feb 27, 2019
Contact name Roger Moorehead
E-mail(s) rmoorehe@uoguelph.ca
Organization name University of Guelph
Department Biomedical Sciences
Street address 50 Stone Rd E
City Guelph
ZIP/Postal code N1G2W1
Country Canada
 
Platform ID GPL15076
Series (1)
GSE120186 Mammary Tissue: aCGH of primary (IGF-IR induced) and recurrent (IGF-IR independent) mammary tumors from MTB-IGFIR mice

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

Data table
ID_REF VALUE
A_67_P04000012 -0.2411101
A_67_P04000019 -0.30086136
A_67_P04000027 -0.8971402
A_67_P04000032 -0.17383339
A_67_P04000058 -0.3965497
A_67_P04000065 -0.2531935
A_67_P04000071 -0.7105664
A_67_P04000083 -0.7259809
A_67_P04000100 -0.091044314
A_67_P04000126 0.37746876
A_67_P04000143 -0.33805713
A_67_P00000082 -1.137382
A_67_P04000179 -0.44745278
A_67_P04000184 -0.08967947
A_67_P04000193 0.007359187
A_67_P04000207 0.1345438
A_67_P00000133 -0.3072777
A_67_P00000149 -0.2040607
A_67_P04000256 -0.15202624
A_67_P00000176 -0.43799624

Total number of rows: 234018

Table truncated, full table size 5976 Kbytes.




Supplementary file Size Download File type/resource
GSM3395631_June25_251469515441_S01_CGH_105_Dec08.txt.gz 67.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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