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