Understanding the interactions between miRNAs and genes they regulate during the acute phase response is crucial to our understanding of inflammatory diseases and processes. Inducing the acute phase response in hepatocytes by stimulating them with interleukin-6 [1] and then examining global changes in mRNA and miRNA expression can provide insight into the timing and dynamics of these interactions. Here we provide additional data for our study, Ref. [2]. In this data, we identify and validate IL-6-induced changes in gene expression [3-6] and their functional relationships over time and between cell types by gene ontology [7,8]. We also provide data showing the enrichment of miRNA binding motifs in the 3׳UTRs of differentially expressed genes [9], and their predicted gene targets derived from our RNA-seq data [10].