Chemical safety screening requires the development of more efficient assays that do not involve testing in animals. In vitro cell-based assays are among the most appropriate alternatives to animal testing for screening of chemical toxicity. Most studies performed to date made use of mRNAs as biomarkers. Recent studies have however indicated the presence of many unannotated non-coding RNAs (ncRNAs) in the transcriptome that do appear to encode proteins. In the present study, we performed whole-transcriptome sequencing analysis (RNA-Seq) to identify novel RNA biomarkers, including ncRNAs, which showed marked responses to the toxicity of nine chemicals. Chemical safety screening was performed in cell-based assays using mouse embryonic stem cell (mESC)-derived neural cells. Marked responses in the expression of some ncRNAs to the chemical compounds were observed. The results of the present study suggested that ncRNAs may be useful in chemical safety screening as novel RNA biomarkers. (C) 2018 Elsevier Inc. All rights reserved.