Single cell mRNA sequencing of Peyer's patch monocyte-derived dendritic cells (LysoDC)

Single-cell RNA-sequencing was used to reveal LysoDC transcriptional plasticity and dynamics of differentiation 23,000 LysoDC were isolated from 246 Peyer's patches from 35 C57BL/6Rj 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 (v2.1.1, default parameters), which performs alignment, filtering, barcode counting and unique molecular identifier (UMI) counting. Reads were aligned to the mouse mm10 genome.