For the HERV RNA-seq analysis (Fig. 1, B and C), eight paired tissues and adjacent normal tissues were collected from the primary sites of patients with TNBC. The samples were immediately snap-frozen and stored at −80°C. To validate TROJAN expression (Fig. 1E), 53 TNBC tumors paired with adjacent normal breast tissue were included. For IHC and quantitative PCR (qPCR) analysis, 153 patients with TNBC (FUSCC cohort 1) who underwent surgery at the FUSCC from 2010 to 2013 were included. For IHC and RNAscope analyses, 200 patients (FUSCC cohort 2) who underwent surgery at the FUSCC from 2001 to 2010 were included. The survival analysis for the TCGA cohort of breast cancer was obtained from GEPIA (Gene Expression Profiling Interactive Analysis; http://gepia.cancer-pku.cn/).

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