Transcriptome analysis was performed on RNA samples of DHSF-BR16 and MCF-7 cells obtained from three independent pellets as reported above .

Gene expression profiling was carried out using the one-color labelling method: labelling, hybridization, slide washing and scanning were performed following the manufacturers protocols (Agilent Technologies). Briefly, mRNA from 100 ng of total RNA was amplified, labeled with Cy3 and purified with columns. Labeled samples (600 ng) were hybridized on Agilent Human Gene Expression 8 × 60 K v3 microarrays. After 17 h, slides were washed and scanned using the Agilent Scanner version C (G2505C, Agilent Technologies). The fluorescence intensities of scanned images were extracted and pre-processed by Agilent Feature Extraction Software (v10.7.3.1).

Differential expression analysis was performed by using the R Bioconductor repository (http://www.bioconductor.org) limma package. Raw intensities were background corrected and normalized with the quantile function. Signals from replicate probes were averaged. Differentially expressed genes (DEGs) were retrieved by combining linear models with empirical Bayes analysis and modified t test raw p values were adjusted for multiple testing by using Benjamini–Hochberg procedure.

DAVID software (Database for Annotation, Visualization and Integration Discovery; http://david.abcc.ncifcrf.gov/) for functional enrichment analysis of the DEGs in DHSF-BR16 cells compared with MCF-7 cells was used. Over-represented Biological Processes, Cellular Components and Molecular Functions of the Gene Ontology (GO) database, as well as KEGG pathways were retrieved by setting to 0.01 the threshold of the enrichment p-value.

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