Comparative Genomic Profiling of Rat Mammary Carcinoma

DNA (1.25 μg) samples from normal ear and mammary carcinoma samples were labeled with cyanine 3- and cyanine 5-dUTP, respectively, and purified using columns (Agilent Technologies, Santa Clara, CA, USA). Labeled DNA was hybridized with microarray probes (Rat CGH, 2×105K; Agilent) at 65°C with rotation at 20 rpm for 40 h, and then washed with Wash Buffers 1 and 2 (Agilent). The microarray resolution was ~14.5 kb (on average) with 97,973 probes, which were annotated in the rn4 version of assembly. Microarrays were scanned using the Agilent G2565BA microarray scanner. Fluorescence intensity values were obtained from scanned images with Agilent Feature Extraction software (ver. 9.5.1, Agilent) and were analyzed using DNA Analytics software (ver. 4.0.81, Agilent). Rat orthologs of human genes relevant to breast cancer [27 (link)] were identified in the rn4 rat genome assembly using the UCSC Genome Browser (https://genome.ucsc.edu/) [28 (link)]. Annotations pertaining to the role of genes in cancer were retrieved from the Oncogene Database (http://ongene.bioinfo-minzhao.org/), Tumor Suppressor Gene Database (https://bioinfo.uth.edu/TSGene/), and COSMIC Database (https://cancer.sanger.ac.uk/census). Microarray data are available at the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo/; accession number GSE160514).

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Nishimura M., Daino K., Fukuda M., Tanaka I., Moriyama H., Showler K., Nishimura Y., Takabatake M., Kokubo T., Ishikawa A., Inoue K., Fukushi M., Kakinuma S., Imaoka T, & Shimada Y. (2021). Development of mammary cancer in γ-irradiated F1 hybrids of susceptible Sprague-Dawley and resistant Copenhagen rats, with copy-number losses that pinpoint potential tumor suppressors. PLoS ONE, 16(8), e0255968.

Publication 2021

Wash Buffers 1 and 2 G2565BA microarray scanner Agilent Feature Extraction software DNA Analytics software

Breast cancer Buffers Cancer Cosmic Dutp Fluorescence Genes Genome Mammary carcinoma Microarray Oncogene Tumor suppressor gene

Corresponding Organization : Tokyo Metropolitan University

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Variable analysis

independent variables

DNA (1.25 μg) samples from normal ear and mammary carcinoma samples

dependent variables

Fluorescence intensity values obtained from scanned images

control variables

Labeled DNA was hybridized with microarray probes (Rat CGH, 2×105K; Agilent) at 65°C with rotation at 20 rpm for 40 h
Microarrays were washed with Wash Buffers 1 and 2 (Agilent)

Annotations

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