Impact of Sequencing Depth and Library Preparation on Toxicological Interpretation of RNA-Seq Data in a "Three-Sample" Scenario.

ABSTRACT: While RNA-sequencing (RNA-seq) has emerged as a standard approach in toxicogenomics, its full potential in gaining underlying toxicological mechanisms is still not clear when only three biological replicates are used. This "three-sample" study design is common in toxicological research, particularly in animal studies during preclinical drug development. Sequencing depth (the total number of reads in an experiment) and library preparation are critical to the resolution and integrity of RNA-seq data and biological interpretation. We used aflatoxin b1 (AFB1), a model toxicant, to investigate the effect of sequencing depth and library preparation in RNA-seq on toxicological interpretation in the "three-sample" scenario. We also compared different gene profiling platforms (RNA-seq, TempO-seq, m

SUBMITTER: Li D 

PROVIDER: S-EPMC7887111 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature