Single-cell transcriptional footprint for the truncated pseudogene SsCLEC9A is associated with antigen processing and presentation in Sus scrofa

FACS to enrich and collect three types of DCs, i.e., cDC1, type 2 DCs (cDC2) and plasmacytoid DCs (pDC), in pig spleen and PBMCs. Four DC subtype marker genes and their fluorescence signals were used to sort these three DCs, i.e., SIRPAlowCADM1+ for cDC1, SIRPA+CADM1+ for cDC2, and SIRPAintIL3RA+CD4+ for pDC , and the enriched cells were subject to bulk RNA-seq analysis.The modifications involved the incorporation of the third exon of the human CLEC9A gene and the removal of the two stop codons name human-like (HL) CLEC9A. HL CLEC9A transcripts were inserted into the pcDNA3.1 vector, with the addition of the 3xFlag protein to produce pcDNA3.1-CLEC9A (HL)-Flag. The empty pcDNA3.1 vector served as the negative control (NC).RNA-seq was performed in these transfected FLT3L-BMHCs with the pcDNA3.1 vector and pcDNA3.1-CLEC9A(HL)-Flag recombinant plasmid to investigate the transcriptomic changes.