We illustrate that 3SEQ can be used for transcriptional profiling to identify both known lncRNAs and novel transcripts within archived primary tissue samples, and our RNA in situ hybridization analysis of one such novel RNA, peak 13741, identified it as an intriguing breast-specific RNA that may be important for the differences between ER+ and ER- breast cancers. This evidence concerns the gene ESR1 and breast cancer.