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Sample GSM3395635 Query DataSets for GSM3395635
Status Public on Nov 28, 2018
Title RJ286_PMT6_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 0.37324318
A_67_P04000019 -0.18623637
A_67_P04000027 -0.05156344
A_67_P04000032 -0.2950919
A_67_P04000058 -0.21911867
A_67_P04000065 0.45494285
A_67_P04000071 -0.13229854
A_67_P04000083 -0.8409241
A_67_P04000100 0.26316583
A_67_P04000126 0.21012023
A_67_P04000143 -6.49E-05
A_67_P00000082 -1.5720527
A_67_P04000179 0.06317658
A_67_P04000184 -0.04019225
A_67_P04000193 0.31567863
A_67_P04000207 0.019430103
A_67_P00000133 0.103383005
A_67_P00000149 0.22309612
A_67_P04000256 -0.8610725
A_67_P00000176 -0.13385682

Total number of rows: 234018

Table truncated, full table size 5965 Kbytes.




Supplementary file Size Download File type/resource
GSM3395635_July_251469511503_S01_CGH_105_Dec08.txt.gz 68.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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