seurat objects for : "scDual-Seq of Toxoplasma gondii-infected mouse bone marrow-derived dendritic cells reveals host cell heterogeneity and differential infection dynamics"

Summary Here, we utilize Dual-scSeq to parse out heterogeneous transcription of bone marrow-derived dendritic cells (BMDCs) infected with T. gondii type I, RH (LDM) or type II, ME49 (PTG) parasites, over multiple time points post-infection (3 and 12h post-infection). Data This repository contains two files, one for each organism investigated (mouse and tgondii), in ".RDS" format generated using Seurat v.4.3.: 1. BMDC_infected_mouse.RDS - object containing normalized read counts (SCT assay) and corresponding metadata for murine BMDCs. metadata columns describe: - orig.ident: plate identity from smartSeq setup - nCount_RNA: UMI count before normalization - nFeature_RNA: Gene count before normalization - nCount_RNA: UMI count before normalization - nUMI: sum of reads per cell for both organisms (mouse + t.gondii) - toxo_nUMI: sum of reads per cell for t.gondii - mouse_nUMI: sum of reads per cell for mouse - nGene: sum of reads per cell for both organisms (mouse + t.gondii) - toxo_nGene: sum of genes per cell for t.gondii - mouse_nGene: sum of genes per cell for mouse - cell_ID: enumerated cells by well - well: well_ID of plate used for smartSeq2 - condition: treatment of cell (one of 8: LDM infection for 3h, LDM infection for 12h, PTG infection for 3h, PTG infection for 12h, LDM Lysate control, PTG Lysate control, uninfected control or LPS control) - percent.mt: percentage of transcript mapped to the mitochondrial genome - cell_ID: enumerated cells by well - nFeature_SCT: Gene count after normalization - nCount_SCT: UMI count after normalization - nFeature_RNA: Gene count before normalization - seurat_clusters: Clusters identified by shared-nearest-neighbor (SNN) inspired graph-based clustering - toxo_clusters: Clusters of t.gondii dataset of the corresponding infected cell - cell type: Annotated subpopulation of infected cells - condition_celltype: condition (see above) combined with celltype (see above) - cluster_celltype: seurat_clusters (see above) combined with celltype (see above) - cluster_condition: seurat_clusters (see above) combined with condition (see above) - UMAP_1: Umap embedding coordinates x-axis - UMAP_2: Umap embedding coordinates y-axis - cell_cycle_phase: predicted cell cycle phase of murine host cells - cycle_phase_t.gondii: predicted cycling phase of t.gondii in the corresponding infected host cell 2. BMDC_infected_tgondii.RDS - object containing normalized read counts (SCT assay) and corresponding metadata for murine BMDCs. metadata columns describe: - orig.ident: plate identity from smartSeq setup - nCount_RNA: UMI count before normalization - nFeature_RNA: Gene count before normalization - nCount_RNA: UMI count before normalization - nUMI: sum of reads per cell for both organisms (mouse + t.gondii) - toxo_nUMI: sum of reads per cell for t.gondii - mouse_nUMI: sum of reads per cell for mouse - nGene: sum of reads per cell for both organisms (mouse + t.gondii) - toxo_nGene: sum of genes per cell for t.gondii - mouse_nGene: sum of genes per cell for mouse - cell_ID: enumerated cells by well - well: well_ID of plate used for smartSeq2 - condition: treatment of cell (one of 8: LDM infection for 3h, LDM infection for 12h, PTG infection for 3h, PTG infection for 12h, LDM Lysate control, PTG Lysate control, uninfected control or LPS control) - percent.mt: percentage of transcript mapped to the mitochondrial genome - cell_ID: enumerated cells by well - nFeature_SCT: Gene count after normalization - nCount_SCT: UMI count after normalization - nFeature_RNA: Gene count before normalization - seurat_clusters: Clusters identified by shared-nearest-neighbor (SNN) inspired graph-based clustering - mouse_clusters: Clusters of mouse dataset of the corresponding infected cell - mouse_celltype: Annotated subpopulation if infected cells - condition_celltype: condition (see above) combined with mouse_celltype (see above) - cluster_celltype: seurat_clusters (see above) combined with mouse_celltype (see above) - cluster_condition: seurat_clusters (see above) combined with condition (see above) - UMAP_1: Umap embedding coordinates x-axis - UMAP_2: Umap embedding coordinates y-axis - cell_cycle_phase_mouse: predicted cell cycle phase of murine host cells - cycle_phase_t.gondii: predicted cycling phase of t.gondii in the corresponding infected host cell