This repository accompanies a study investigating the immune mechanisms underlying Plasmodium-induced lung injury, with a particular focus on the role of IFN-γ signaling in T cells and its impact on T cell–monocyte interactions and pulmonary pathology.
Key approaches:
- Bulk RNA-seq and spatial transcriptomics performed on a murine Plasmodium lung infection model to map the temporal and spatial dynamics of immune responses.
- scRNA-seq from a MA-ARDS model used to validate immune cell subsets and regulatory interactions.
The datasets provided enable a comprehensive, multi-dimensional exploration of the host immune landscape during Plasmodium infection.
This repository contains raw count matrices and R scripts for analyzing bulk RNA-seq, single-cell RNA-seq, and spatial transcriptomics data.
Data include multiple time points, as well as pre- and post-infection conditions, allowing in-depth investigation of immune responses in Plasmodium-induced lung injury.
- 01_Bulk_DEGs.Rds, 01_Bulk_Matrix.Rds, 01_Bulk_SampleTable.Rds — Bulk RNA-seq data, including differential expression results and sample information.
- 01_biomart_hom_mus_gene.Rds — Gene annotation from Biomart, including homologous gene mappings for Mus musculus.
- 02_01_scedata.Rds, 02_01_scedata_Normaldata.Rds, 02_01_scedata_PCA.Rds, 02_01_scedata_UMAP.Rds — Single-cell RNA-seq data with normalized counts and dimensionality reduction results (PCA, UMAP).
- 03_01_Infect.Rds, 03_01_Infect_Ifngr1KO.Rds, 03_01_Uninfect.Rds — Spatial transcriptomics data for infected, Ifngr1KO, and uninfected samples for comparative analysis.
Bulk RNA-seq Analysis
01_Bulk_RNAseq_01_SampleDistance.Rmd— Sample distance analysis.01_Bulk_RNAseq_02_DEG.Rmd— Differential expression analysis (DESeq2).01_Bulk_RNAseq_03_Mfuzz.Rmd— Time-series clustering using Mfuzz.01_Bulk_RNAseq_04_Xcell.Rmd— Cell type enrichment with Xcell.
Single-cell RNA-seq Analysis
02_ScRNAseq_01_Quantity.Rmd— Immune cell quantification.02_ScRNAseq_02_DEG.Rmd— Differential expression analysis.02_ScRNAseq_03_NicheNet.Rmd— Cell–cell communication analysis (NicheNet).
Spatial Transcriptomics Analysis
03_SpatialData_01_CCA.Rmd— Batch integration using Canonical Correlation Analysis (CCA).03_SpatialData_02_SubRegion.Rmd— Sub-region analysis.03_SpatialData_03_Deconvolution.Rmd— Cell type deconvolution.
If you use the data or code from this repository, please cite as:
Chen S, Yang Q, Zhong Y, Liu D, Zhou L, Wei H, Li C,Song J, Wang Y, Hu X, Chen L, Lin J.0.Comprehensive immune profiling reveals IFN-γ signaling in T cells mediates parasite phagocytosis in a rodent malaria model. mBio0:e03938-25.https://doi.org/10.1128/mbio.03938-25.