Transcriptomic Profiling of CD11c+ T Cells

Microarray gene expression profiling with Mouse Genome 430 PM Strip arrays was performed following manufacturer recommendations (Affymetrix Inc, Santa Clara, CA) with specific adaptations based on the picoprofiling method [18 (link)]. Image intensities were extracted with Affymetrix GeneAtlas System software, normalized and summarized by RMA and analyzed for differential gene expression by Limma [19 ] with false discovery rate multiple testing significance correction. NK-related γδTCR, iNKT CD4⁺ and iNKT CD4^- cells specific gene sets [20 (link)] were tested by Gene Set Enrichment Analysis (GSEA) [21 (link)] for significant enrichment in CD11c⁺ T cells.