Comparative Transcriptomic Analysis of Trypanosoma cruzi Strains G and Y

Overview

This repository contains the bioinformatics pipeline and downstream analysis scripts for comparing the gene expression profiles of two Trypanosoma cruzi strains: Strain G (TcI) and Strain Y (TcII).

While the raw data originates from a study on P21 ablation (Silveira et al., 2025), this specific analysis focuses exclusively on the wild-type (control) samples to elucidate strain-specific transcriptional differences, excluding the knockout samples.

Study Context

• Organism: Trypanosoma cruzi
• Strains: G (TcI) vs Y (TcII)
• Reference Genome: T. cruzi strain G (TriTrypDB Release 64).

Repository Structure

├── data/
│   ├── dados_cepag/               # Count tables for Strain G
│   ├── dados_cepay_ref_cepag/     # Count tables for Strain Y
│   ├── refs/                      # Reference files from TriTrypDB
│   │   └── TriTrypDB-64_TcruziG.gtf
│   └── TriTrypDB-64_TcruziG_GO.gaf # Gene Ontology annotations from TriTrypDB
├── results/
│   ├── figures/                   # Output plots
│   ├── tables/                    # Differential expression tables
│   └── deseq2_dds.rds             # Saved DESeq2 object
└── index.qmd                      # Quarto notebook compiling the full analysis

Prerequisites

To run the analysis, you need R (>= 4.0) and the following packages:

# CRAN
install.packages(c("tidyverse", "ggplot2", "pheatmap", "openxlsx", "patchwork", "svglite", "RColorBrewer", "forcats"))

# Bioconductor
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(c("DESeq2", "rtracklayer", "GO.db", "AnnotationDbi"))

Data Availability

This analysis utilizes data associated with the following publication:

Silveira, A. C. A., et al. (2025). P21 Ablation Unveils Strain‐Specific Transcriptional Reprogramming in Trypanosoma cruzi Amastigotes. International Journal of Microbiology. DOI: 10.1155/ijm/9919200