Joint analysis of scRNA-seq from the IDC stages of P. falciparum and P. berghei led to the identification of a gene involved in lipid metabolism, named CAP. Experimental evidence indicates that CAP mediates its biosynthesis of phosphatidylcholine and phosphatidylethanolamine through interaction with the host CTL1.
The project includes raw count matrices and R scripts to analyze scRNA-seq of P. falciparum and P. berghei parasite cells, along with bulk RNA-seq for CAP Knockout in P. berghei. For lipidomics analysis, we exclusively used MetaboAnalystR.
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Data
01_01_Pb_seurat.Rds, 01_02_Pf_seurat.Rds: SeuratObject of P. falciparum and P. berghei. Raw count matrices of scRNA-seq from MCA.
02_Gene_Orth_Data.xlsx: One-to-one orthologs across ten Plasmodium species. 03_LipidGene.xlsx: Gene involved in lipid metabolism of P. falciparum.
04_RF_GeneInfo： Gene information for random forest.
05_raw_counts.txt: raw count matrices of bulk RNA-seq. -
Analysis
03_01_pb_cl.Rds, 03_02_pb_df.Rds, 03_03_pb_Mfuzzgene.Rds: SeuratObject of P. falciparum.
03_04_pf_cl.Rds, 03_05_pf_df.Rds, 03_06_pf_Mfuzzgene.Rds: SeuratObject of P. berghei. -
Script
01_Scmap_Related_Fig1.Rmd: Scmap performed stage clustering of single-cell transcriptomic data.
02_Expression_LipidGene_Related_FigS1.Rmd: ComplexHeatmap demonstrated the dynamics of conserved lipid metabolism-related genes.
03_Mfuzz_Related_Fig1.Rmd: Mufzz analysis found the genes with high expression in the mid- and late- trophozoite stages.
04_Randomforest_Related_Fig1.Rmd: RandomForest analysis calculated lipid metabolism-related score for unknown function genes.
05_DESeq2_Related_Fig3.Rmd: DESeq2 analyzed the transcriptome differences after CAP knockout.