Single-cell transcriptomic analysis of mouse lung CD11b+ dendritic cells post allergic sensitization

Conventional dendritic cells (cDCs) in the lung that drive effector T cell differentiation, and initiate allergic responses upon inhalation of allergens. However, since CD11b+ cDCs are heterogeneous, the specific function of each subpopulation has been elusive. To identify subpopulations of CD11b+ cDCs, we performed single cell RNA-sequencing (scRNAS-Seq) of total lung CD11b+ cDCs following inhalation of house dust extracts, and detected multiple clusters based on their differential transcriptomes. The data will be applicable for studies of cDC function in induction of T cell differentiation as well as the maturation pathway of cDCs. CD11b+ cDCs (CD45+ CD11c+ I-A+ Siglec-F– CD88– F4/80– CD103– Live/Dead–) from C57BL/6 mice inhaled house dust extract together with ovalbumin were loaded into the Single Cell Chip followed by forming single cell. The Gene Expression library and the ADT Library were prepared using the Chromium single cell 3′ v2 library and gel bead kit (10x Genomics) and additional reagents recommended in the protocol of Total A-seq (Biolegend). The two libraries were mixed at 10:1 molar ratio (Gene Expression library to ADT library) and sequenced by the NIEHS Epigenomics and DNA Sequencing Core Laboratory on NextSeq 500 (Illumina) with paired-end sequencing (Read 1: 31; Read 2: 101).