We performed flow cytometry, bulk, and single-cell RNA-sequencing to profile ileal lamina propria and intraepithelial CD4 T cells (CD4CD8αα, regulatory T cells (Tregs), CD69− and CD69high Trm T cells) in controls and Crohn’s disease (CD) patients (paired non-inflamed and inflamed). The gene discussed is CD69; the disease is Crohn disease.