A Pipeline for High-Throughput Concentration Response Modeling of Gene Expression for Toxicogenomics.

ABSTRACT: Cell-based assays are an attractive option to measure gene expression response to exposure, but the cost of whole-transcriptome RNA sequencing has been a barrier to the use of gene expression profiling for in vitro toxicity screening. In addition, standard RNA sequencing adds variability due to variable transcript length and amplification. Targeted probe-sequencing technologies such as TempO-Seq, with transcriptomic representation that can vary from hundreds of genes to the entire transcriptome, may reduce some components of variation. Analyses of high-throughput toxicogenomics data require renewed attention to read-calling algorithms and simplified dose-response modeling for datasets with relatively few samples. Using data from induced pluripotent stem cell-derived cardiomyocytes t

SUBMITTER: House JS 

PROVIDER: S-EPMC5672545 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature