These RDS files contain DESeqDataSet objects subset into broiler groups of 4, 12 and 33 days post-hatch. These objects are the result of DESeq2::DESeq( … ,betaPrior=FALSE).The .txt-objects contain the normalized sequencing counts per broiler age group. These objects are the result of DESeq2::counts( … , normalized=TRUE). Data was generated using STAR v2.7.9a and DESeq2 v1.34. Metadata is included as Excel file. Sequencing data is deposited at NCBI-SRA under BioProject: PRJNA949454. Study abstract Dirkjan Schokker, Soumya K. Kar, Paul Stege, Norbert Stockhofe, Alex Bossers, Vera Perricone, Annemarie Rebel, Ingrid de Jong Gut health is a prerequisite for broiler welfare. In this study, we investigated the effect of three dietary interventions on small intestinal development in broilers and special emphasis on immunity. Morphometry and immunostaining showed no significant differences in any of the treatments, however, gene expression revealed significant differences in the LPHF and MCFA treatments. Pathway enrichment analysis showed a few main pathways involved in regulation of cellular processes, cell structural processes, and cell protection, as well as a putative link to inflammatory processes. Taken together, these findings suggest that dietary interventions can modulate gut health and functionality in chicken.