High-throughput Transcriptomics Screen of 313 Reference Chemicals in U-2 OS Cells
High-throughput transcriptomics (HTTr) was undertaken to quantify and characterize the biological effects of chemicals observed in human-derived in vitro test systems. RefChemDB (Judson et al., 2019), a database that links chemicals to molecular targets with which they interact, was used to select a set of 313 chemicals linked to a diverse set of targets. These chemicals were tested using the HTTr assay in eight point dilution series in the human-derived cell type U-2 OS (osteosarcoma). Chemicals were randomized to treatment plates containing cells cultured in growth media. All chemicals were tested in triplicate using three independent U-2 OS cultures. Assay plates also contained reference treatments for quality control purposes. The TempO-Seq human whole transcriptome assay (Yeakley et al., 2017) was used to characterize the biological activity of test chemicals. Raw counts were processed with EPA's High Throughput Transcriptomics Pipeline (httrpl), which includes read alignment, QC evaluation, outlier exclusion, and differential expression analysis with DESeq2 (Love et al., 2014). For chemicals with molecular targets expressed in U-2 OS cells, the data may be used to generate gene expression profiles that are indicative of molecular target activation or disruption.