The efficacy of 17 β-estradiol (E2) was valid in some cancers, while its effects on squamous cell lung carcinoma (SCLC) were still unclear. The aim of our study was to investigate the potential targets and molecular mechanisms of E2 in SCLC cells.Two RNA libraries from human lung carcinoma cells (SK-MES-1) with and without E2 treatment were constructed and sequenced. The differentially expressed genes (DEGs) between cells with or without E2 treatment were identified by cuffdiff software. Hierarchical Clustering Analysis (HCA) was performed for displaying gene expression changes and classification. Furthermore, enrichment analyses of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology Biological Process (GO BP) terms were performed through DAVID. The protein-protein interaction (PPI) network was constructed through STRING. Additionally, differentially expressed lncRNAs were also selected by cuffdiff software.Total 129 DEGs including 58 up-and 71 down-regulated genes were obtained. Cancer-related pathways including small cell lung cancer, hypertrophic cardiomyopathy (HCM) and pathways in cancer and biological processes including regulation of phosphorus metabolic process, protein localization and nucleus organization were enriched. The PPI network with 113 nodes and 312 edges was constructed. CASP3, ITGA2, COL4A6, PML and CDC25B were identified as hub nodes which had more interactions with others in the PPI network. Furthermore, eight up-regulated and ten down-regulated lncRNAs were selected.CASP3, ITGA2 and Lnc-DLK1-4:31 (one of down-regulated lncRNAs) might play pivotal roles in E2 treated SCNC cells by influencing cell apoptosis, angiogenesis and cell invasion respectively.Key words: squamous cell lung carcinoma, RNA-Seq, differentially expressed genes, lnc-RNA Squamous cell lung carcinoma (SCLC) is a common type of non-small-cell lung cancer (NSCLC) and the second leading cause of death related to lung cancer which causes approximately 400,000 deaths per year worldwide [1]. SCLC develops mainly in the upper airways and cigarette smokers are more susceptible to SCLC, therefore it is more common in men than in women [2]. Although various therapies such as radiation, chemotherapy, surgery and palliative care have been used for SCLC treatment, the overall therapeutic results were not optimistic [3,4]. A more thorough understanding of the mechanism of SCLC may offer a new hope on treatment innovations and prevention strategies.Estrogens are a group of human sex hormones which can be secreted primarily by the ovaries and placenta in women and the testes in men. The cell response to estrogens is in a concentration-dependent manner. Previous studies found that low concentration of 17 β-estradiol (E2) promoted the development of breast cancer and prostatic cancer, while 10 nM or higher concentration of E2 could cause cancer cell apoptosis [5][6][7]. The three major naturally occurring estrogens are E2, estrone and estriol, among them, E2 is the predominant and most active [8]. Meanwhile, Zhao et al...