Gene expression data of Peyer's patch conventional dendritic cells and macrophages at steady state and under TLR7 ligand stimulation

The initiation of the mucosal immune response in Peyer’s patch (PP) relies on the sampling, processing and efficient presentation of foreign antigens by dendritic cells (DC). PP DC encompass five subsets, among which CD11b+ conventional DC (cDC) and LysoDC have distinct progenitors and functions but share many cell surface markers. This has previously led to confusion between these two subsets. In addition, another PP DC subset, termed double-negative (DN), remains poorly characterized. Here, we have studied the genetic relatedness of the different subsets of PP cDC at steady state and under TLR7 ligand stimulation. We also provide the transcriptional profiles of subepithelial TIM-4- and interfollicular TIM-4+ macrophages. Three independent replicates of TIM-4- and TIM-4+ LysoMac, CD8a+ and DN dome cDC and five independent replicates of CD11b+ dome cDC were sorted from Peyer's patch of C57BL/6 mice at steady state. In addition, three and five independant replicates of CD11b+ and CD8a+ dome cDC, respectively were sorted from Peyer's patch of C57BL/6 mice 9 hours after R848 gavage. Total RNA of Peyer's patch sorted cells was extracted with a Qiagen RNeasy Plus Micro Kit. Quantity, quality and absence of genomic DNA contamination were assessed with a Bioanalyser (Agilent). Microarray experiments were performed by the Plateforme Biopuces of Strasbourg (France) using the Affymetrix GeneChip® Mouse Gene 1.0 ST Array.