RNA-seq profiling of plasmacytoid and conventional dendritic cells from wildtype and PU.1 knockout mice

Dendritic cells (DCs) are can be broadly divided into conventional (cDC) and plasmacytoid (pDC) subsets. Despite the importance of this lineage diversity, its genetic basis is not fully understood. RNA-seq gene expression analysis of wild type (WT) and PU.1 transgenic mice revealed a key role for PU.1 in maintaining cDC identity. Itgax-Cre mice were crossed to Spi1(fl/fl) mice allowing Spi1 (PU.1) inactivation in CD11c expressing cells. Dendritic cells (DCs) were enriched from the spleen using CD11c magnetic beads.Conventional DCs (CD11c+MHCII+NK1.1-CD19-SiglecH-) and plasmacytoid DCs (CD11c+Bst2+SiglecH+ NK1.1-CD19-) were isolated from the spleens of wild type (WT), PU.1+/- heterozygous and PU.1-/- homozygous knockout mice. RNA was isolated independently from 2 biological replicates for each genotype and cell subset. Transcription was profiled by RNA-seq for all 12 samples on a HiSeq 2500 at the Australian Genomic Research Facility to generate 100 base-pair single-end reads.