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The adult small intestine contains more than half of the body's lymphocytes in order to maintain homeostasis with the commensal microbiota. Birth marks a transition of the intestine from a sterile to an increasingly colonized environment. The data described in this article are incremented into the work published by Torow et al. titled "Active suppression of intestinal CD4(+) TCRαβ(+) T lymphocyte maturation during the postnatal period" [1]. While most of the CD4 T cells found in the adult small intestine have an activated phenotype marked by expression of helper lineage specific genes neonatal lymphocytes exhibit a naïve phenotype. Further, direct comparison of neonatal CD4 T cells from the small intestine and the gut draining mesenteric lymph node (mLN) reveals a global transcriptional 'inactivity' of the small intestinal CD4 T cells. Here, we describe in more detail the experimental design, sample preparation and analysis that were performed to obtain and interpret the microarray data. The data set is publicly available through the Gene Expression Omnibus (GEO) database with accession number GSE60515, and the analysis and interpretation of these data are included in Torow et al. [1].

Transcriptional profiling of intestinal CD4+ T cells in the neonatal and adult mice