Gene expression in the adult zebrafish intestine during starvation and refeeding

In this RNA-Seq dataset, we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA-Seq data revealed starvation-induced alterations in transcript levels for many genes, including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days after starvation was sufficient to restore most transcripts to their baseline pre-starvation levels. These host RNA-Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish (81dpf, days post-fertilization) that were separately housed. One treatment group (control) was continuously fed throughout the study, while the experimental group was starved for up to 21 days and then refed. At each timepoint (3dpS = 3 days post-starvation; 21dpS = 21 days post-starvation; 3dpR = 3 days post-refeeding), 4 zebrafish were taken from each treatment group, euthanized, and dissected to remove the whole intestine for RNA extraction and RNA-Seq analysis.