Single cell mRNA sequencing of Peyer's patch CD11c+ phagocytes from unstimulated or R848- or CpG-stimulated mice

We deciphered the transcriptional landscape of Peyer's patch CD11c+ phagocytes from their emergence in the tissue to their final maturation state at homeostasis and under stimulation with the TLR7 ligand R848 and the TLR9 ligand CpG. cDC1s, cDC2s, LysoDCs and macrophages were isolated from Peyer's patches of 12 untreated, 12 R848-treated and 12 CpG-treated C57BL/6Rj female mice and processed using the Chromium Single Cell 3’ kit from 10X genomics (California, USA) for the library preparation and the NextSeq 500/550 High Output Kit v2 (75 cycles) cartridges from Illumina for the sequencing. FASTQ raw files were processed using Cell Ranger software, which performs alignment, filtering, barcode counting and UMI counting. Reads were aligned to the mouse mm10 genome.