This dataset contains the data required to reproduce the analysis and the figures in the paper: Gene expression changes in ducklings exposed in ovo to emerging per-/poly-fluoroalkyl substances PFDoDS and PFECHS.

This study investigated the effects of two emerging PFAS compounds, perfluoro-4-ethylcyclohexane sulfonic acid (PFECHS) and perfluorododecane sulfonic acid (PFDoDS), alongside legacy perfluorooctanesulfonate (PFOS), on gene expression in the liver, heart, and bursa of Fabricius from mallard ducklings (Anas platyrhynchos) exposed in ovo. These PFAS compounds were selected based on their detection in a declining sea duck species and concerns over their endocrine disruption potential. Farmed mallard eggs were injected with environmentally relevant concentrations of PFECHS, PFDoDS and the regulated PFOS. In the liver, mRNA and smallRNA sequencing revealed sex-specific changes in genes related to metabolism and immune function, particularly those involved in antiviral responses, in PFECHS- and PFDoDS-exposed ducklings. In the heart, targeted qPCR analysis of mRNA and microRNA associated with stress, inflammation, and development showed no statistically significant differences, though trends included altered expression of genes involved in oxidative and cellular stress responses across treatments. In the bursa of Fabricius, targeted qPCR of immune-related mRNA revealed upward trends in innate immune gene expression across all exposure groups, also consistent with antiviral immune activation. These findings demonstrate that emerging PFAS exposure alters gene regulation related to key physiological pathways, with responses differing by sex and tissue type. Our results underscore the complexity of PFAS-induced immune modulation and highlight potential developmental risks of maternal PFAS transfer in wild avian species.