RNAseq of renal dendritic cells from adult Clec9a-Cre Rosa-YFP mice

We use bulk RNA sequencing of sorted cells to characterize the gene expression profiles of renal dendritic cell (DC) subsets, cDC1 and cDC2, as well as MHCII+CD64+ F4/80hi and MHCII+CD64+ CD11bhi cells. Splenic DCs and red pulp macrophages serve as reference populations for a macrophage-like or DC-like phenotype. By sorting YFP+/YFP- F4/80hi or YFP+/YFP- CD11bhi cells from Clec9a-Cre Rosa-YFP mice we aim to reveal transcriptional differences between YFP-labelled and unlabelled cells. We showed that F4/80hi cells resemble macrophages on a transcriptional level, despite their DC origin, and that renal CD11bhi cells are a transcriptionally unique subset. However, we were not able to reveal differences between YFP+ and YFP- populations. RNAsequencing of murine dendritic cell and macrophage populations from kidney and spleen