IMPI-3: Bulk RNA-Seq analysis

People involved:
Principal Investigator: Mpiko Ntsekhe, Robert Wilkinson
Bioinformatics Support Team: Kuhle Mcinga, Ephie Geza, Mohammed Farahat
Support Requested: Rob Rousseau

Short description of the project:
This clinical trial is a unique opportunity to comprehensively measure and compare Mycobacterium tuberculosis (Mtb) responding immune responses(including conventional & unconventional T cell response as well as innate response) in blood and at the site of the Pericardial Fluid (PCF).

Objectives:

1. Compare RNA-Seq data using blood taken at baseline to the end of treatment. To see how anti-tuberculosis therapy (ATT) affects the transcriptional signatures in blood sampling.
2. Compare the RNA-Seq data from PCF to blood.
3. Compare PCF collected at baseline compared to PCF collected at day 1-3. This will grant us insight into how ATT affects transcriptional signatures in patients with Pericardial TB.