Reanalysis of RNA-seq data from human cutaneous lesions infected with Leishmania amazonensis (SRA SRP069976)

This repository contains processed transcriptomic data and analysis outputs generated from the reanalysis of publicly available RNA-seq data derived from human cutaneous lesions infected with Leishmania amazonensis (NCBI SRA accession SRP069976, Christensen et al., 2019). Raw sequencing reads were downloaded from the Sequence Read Archive and processed from scratch. Transcript quantification was performed using Salmon (v1.10.3) against the GENCODE v48 (GRCh38) transcriptome. Gene-level counts were generated using tximport, and downstream differential expression analyses were performed using DESeq2 in R. The deposited materials include normalized expression matrices, differential expression results, selected gene expression tables used for visualization, and R scripts used for data processing and analysis. Raw sequencing data are publicly available from the NCBI Sequence Read Archive under accession SRP069976. These data support the analyses presented in the associated manuscript currently under submission investigating the role of the aryl hydrocarbon receptor (AhR) in host responses to Leishmania amazonensis infection