Ester-16/BSPZV1-malaria-vaccine-RNAseq

RNA-seq analysis of PfSPZ vaccine trial in Tanzania # BSPZV1-malaria-vaccine-RNAseq Analysis RNA-seq analysis of PfSPZ vaccine trial in Tanzania ## About This Project This project analyzes whole blood RNA-seq data from the BSPZV1 Phase 1 clinical trial that evaluated the PfSPZ malaria vaccine in Tanzania. The vaccine uses live, radiation-attenuated Plasmodium falciparum sporozoites (PfSPZ) administered intravenously to healthy male volunteers aged 18 to 35 years in Tanzania. The goal of this analysis is to explore gene expression patterns across vaccine trial participants using basic data science tools in R. ## Dataset - **Source**: GEO public database (GSE196126) - **Organism**: Homo sapiens - **Samples**: 172 whole blood samples - **Genes**: 15,297 after quality filtering - **Data type**: Raw RNA-seq counts ## What This Analysis Does ### Script 1 — Load and Explore (01_load_explore.R) - Loads the raw count matrix from Excel - Checks the dimensions of the dataset - Explores gene names and sample IDs - Checks for missing values ### Script 2 — Clean and Filter (02_clean_filter.R) - Renames columns for clarity - Filters out genes with fewer than 10 total counts - Calculates library sizes per sample - Saves cleaned data as CSV files ### Script 3 — Visualisation and Statistics (03_visualise.R) - Creates a barplot of library sizes across all 172 samples - Plots the distribution of CD8A gene expression - Creates a scatter plot comparing CD8A vs IFNG expression - Runs a linear regression to test if CD8A predicts IFNG expression ## Key Findings - The dataset contains 15,297 genes across 172 blood samples - Average library size per sample was approximately 11 million reads - CD8A (T cell marker) and IFNG (interferon gamma) showed a statistically significant positive correlation (p-value = 2.37e-08, R-squared = 0.168) - This suggests that samples with more T cells tend to produce more interferon gamma, which is biologically important for malaria immunity ## Tools and Packages Used - **R** — statistical programming lan …