Differential gene expression and functional enrichment datasets from rainbow trout (Oncorhynchus mykiss) exposed to municipal wastewater treatment plant effluent

This repository contains transcriptomic analysis results generated from rainbow trout (Oncorhynchus mykiss) exposed to municipal wastewater treatment plant (WWTP) effluent under environmentally realistic field conditions. The dataset accompanies the manuscript: Rainbow Trout (Oncorhynchus mykiss) as a Model Organism for Assessing Long-Term Impacts of Municipal Wastewater Pollution on Early Fish Development Fish were collected from an upstream reference site (Site C) and a downstream WWTP-affected site (Site E) after five months of field exposure. RNA sequencing was conducted on six tissues (gills, brain, pituitary, liver, kidney, and gonads). A total of 96 RNA-seq libraries were generated, of which 94 passed quality control and were included in downstream analyses. Differential gene expression analyses were performed between Site C and Site E using a negative binomial model. Genes with an adjusted p-value < 0.05, |log₂FoldChange| > 1, and baseMean > 5 were considered significantly differentially expressed. Functional interpretation was conducted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Repository contents: • DEG_results.xlsx – Differentially expressed genes. • GO_enrichment.xlsx – GO enrichment results. • KEGG_enrichment.xlsx – KEGG pathway enrichment results. • README.txt – Dataset documentation. • Metadata.xlsx – Experimental metadata.