Joint analysis of bulk RNA-seq, scRNA-seq, and spatial transcriptomics in MA-ARDS

The project involves a multi-dimensional transcriptomic analysis to uncover key immune cells in Malaria-associated Acute Respiratory Distress Syndrome (MA-ARDS). Our analysis includes bulk RNA-seq data from different time points, scRNA-seq data pre- and post-infection, and spatial transcriptomic data. We provide quantitative transcriptomic data across all dimensions in this repository.

Script guidance

The project includes raw count matrices and R scripts to analyze bulk RNA-seq, single-cell RNA-seq, and spatial transcriptomics data. We provide data from multiple time points, as well as pre- and post-infection conditions, to allow comprehensive exploration of immune responses in MA-ARDS.

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1) Data

• 01_Bulk_DEGs.Rds, 01_Bulk_Matrix.Rds, 01_Bulk_SampleTable.Rds: Bulk RNA-seq data matrices, including differential gene expression analysis and sample information.
• 01_biomart_hom_mus_gene.Rds: Gene annotation data from Biomart, including homologous gene information 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, including normalized data and dimensionality reduction (PCA, UMAP) results.
• 03_01_Infect.Rds, 03_01_Infect_Ifngr1KO.Rds, 03_01_Uninfect.Rds: Spatial transcriptomics data of infected, Ifngr1KO, and uninfected samples for comparative analysis.

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2) Script

• 01_Bulk_RNAseq_01_SampleDistance.Rmd: Analysis of sample distance in bulk RNA-seq data.
• 01_Bulk_RNAseq_02_DEG.Rmd: Differential expression analysis using DESeq2.
• 01_Bulk_RNAseq_03_Mfuzz.Rmd: Mfuzz clustering analysis for temporal gene expression patterns.
• 01_Bulk_RNAseq_04_Xcell.Rmd: Cell type enrichment analysis using Xcell.
• 02_ScRNAseq_01_Quantity.Rmd: Quantification of immune cell types in scRNA-seq data.
• 02_ScRNAseq_02_DEG.Rmd: scRNA-seq differential expression analysis.
• 02_ScRNAseq_03_NicheNet.Rmd: Cell-cell communication analysis using NicheNet.
• 03_SpatialData_01_CCA.Rmd: Batch Integration Using Canonical Correlation Analysis (CCA) for Spatial Transcriptomics Data.
• 03_SpatialData_02_SubRegion.Rmd: Sub-region analysis of spatial transcriptomics data.
• 03_SpatialData_03_Deconvolution.Rmd: Deconvolution of spatial transcriptomics data.

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