Evaluation of Sequencing Approaches for High-Throughput Transcriptomics – (BOSC)

Whole-genome in vitro transcriptomics has shown the capability to identify mechanisms of action and estimates of potency for chemical-mediated effects in a toxicological framework, but with limited throughput and high cost. The generation of high-throughput global gene expression profiles using RNA-sequencing technologies for the evaluation of chemically-mediated effects could greatly advance the current toxicogenomics knowledgebase. We present the evaluation of three transcriptomics platforms for potential application to high-throughput screening: 1. TempO-Seq utilizing custom designed paired probes per gene; 2. Targeted sequencing utilizing Illumina’s TruSeq RNA Access Library Prep Kit containing tiled exon-specific probe sets; 3. Low coverage whole transcriptome sequencing using Illumina’s TruSeq Stranded mRNA Kit. In summary, the three transcriptomics platforms showed the ability to measure whole-genome transcript levels with good technical reproducibility and show promise for the integration of transcriptomics into high-throughput screening.