Single-cell RNA-sequencing of thymic myeloid cells from Csf1rgfp/gfp (MaFIA) and Cd11cyfp/yfp mice

Purpose: The goals of this study are to identify different sub-populations of mouse thymic myeloid cells and to compare their differentially expressed genes. Methods: Single-cell mRNA libraries of EGFP-positive and YFP-positive cells from 5-weeks-old Csf1rgfp/gfp and 9-weeks-old Cd11cyfp/yfp mice were generated with Chromium X (10X Genomics), in two biological replicates, each, followed by sequencing using Illumina NovaSeq. The sequence reads that passed quality filters were aligned against Ensembl GRCm39 mouse genome assembly with GRCm39.104 annotation by STARsolo, downsampled by DropletUtils, and analyzed by SingleCellExperiment. Results: we obtained about 1 billion sequence reads per sample, except for 1 sample (MaFIA rep1), which contained reads mostly derived from mitochondria and was excluded from downstream analysis. In the other three samples, over 90% of reads had valid barcodes and reached sequencing saturation about 70%. Over 80% of reads could be mapped to mouse genome uniquely (build GRCm39). Each sample had estimated number of cells over 6,000. Downstream analysis identified different subsets of thymic macrophages and dendritic cells, along with small amount of plasmacytoid dendritic cells, T cells and B cells, all of these populations could be clearly clustered and presented on tSNE or UMAP. Conclusions: We could identify 4 populations of dendritic cells, 2 populations of macrophages and one monocyte population in the thymus. This dataset is a rich resource for exploring the diversity of thymic myeloid cells at single cell resolution. Transcriptional profiling of thymic macrophages at single-cell level, generated from single-cell preparation of the MaFIA and CD11c-YFP mouse thymus EGFP or YFP positive cells, sequenced in several batches on illumina NovaSeq platform.