Cells derived from mLN or CoLP of Control WT (Notch2fl/fl), Control Re-derived Notch2cKO (Notch2fl/fl CD11cCre+), dysbiotic WT (Notch2fl/fl CD11cCre-) and dysbiotic Notch2cKO (Notch2fl/fl CD11cCre+) mice were individually multiplexed by labeling each cell suspension with a unique Hashtag (HTO) antibody. Per biological replicate, ~37K mLN and ~3K CoLP sort-purified CD26+CD11c+MHCII+ dendritic cells, pooled across all genotypes and conditions, were loaded onto a 10x Genomics Chromium Single Cell Controller. Single cell capture, cDNA and library preparations were performed with the Single Cell 3' v4 Reagent Kit (10x Genomics) according to manufacturer's instructions. GEX and HTO sequencing libraries were loaded on an Illumina NovaSeq 6000 with high output cycle kits and sequenced paired-end using the following read configuration:150-10-10-150 (R1-I1-I2-R2). R2 contains the 15bp HTO barcode sequence.