title: Illumina HiSeq 4000 paired end sequencing; RNA-seq of human ovarian adenocarcinoma cell line SKOV3 treated with bisphenol A (10 or 100 nM) against untreated controls
design: RNA-seq of human ovarian adenocarcinoma cell line SKOV3 treated with bisphenol A (10 or 100 nM) against untreated controls
library_construction_protocol: Human ovarian adenocarcinoma cell line SKOV3  was purchased from the Cell Bank of the Chinese Academy of Sciences (Shanghai, China), and SKOV3 has been authenticated using short tandem repeat (STR) profiling. Human ovarian adenocarcinoma SKOV3 cells were exposed to bisphenol A (10 or 100 nM) or 0.1% DMSO for 24 h. Human ovarian adenocarcinoma SKOV3 cells were treated with BPA (10 or 100 nM) or DMSO for 24 h, and then cells were washed twice with phosphate-buffered saline (PBS), total RNA was extracted from cells using Trizol reagent (Sangon Biotech) according to the manufacturer's instructions. The RNA degradation and contamination was monitored on 1% agarose gels, and the purity and concentration of final RNA was checked using the NanoPhotometer spectrophotometer (IMPLEN) and Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies), respectively. The integrity of total RNA samples was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies). Finally, a total amount of 3 μg RNA with A260/A280 ratios between 1.9 and 2.1 and RNA integrity number (RIN) above 7.5 was equally pooled from each sample for cDNA library construction. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.