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Sample GSM3395636 Query DataSets for GSM3395636
Status Public on Nov 28, 2018
Title RJ236_PMT7_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 -0.15419507
A_67_P04000019 -0.007140213
A_67_P04000027 -0.94232285
A_67_P04000032 -0.31003645
A_67_P04000058 -0.13568877
A_67_P04000065 -0.30141836
A_67_P04000071 -0.32827967
A_67_P04000083 -0.8446829
A_67_P04000100 -0.11427329
A_67_P04000126 0.22847775
A_67_P04000143 -0.4306533
A_67_P00000082 -1.2670155
A_67_P04000179 -0.12821136
A_67_P04000184 0.16112974
A_67_P04000193 0.23708615
A_67_P04000207 -0.12489175
A_67_P00000133 -0.37534422
A_67_P00000149 0.2983787
A_67_P04000256 0.09549316
A_67_P00000176 0.45798585

Total number of rows: 234018

Table truncated, full table size 5985 Kbytes.




Supplementary file Size Download File type/resource
GSM3395636_July_251469511504_S01_CGH_105_Dec08.txt.gz 67.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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