READ ME File For 'Overall Thesis Data'

Dataset DOI: 10.5258/SOTON/D2990

ReadMe Author: Patrick Trimby-Smith, University of Southampton, https://orcid.org/0009-0004-6041-611X

This dataset supports the thesis entitled: Exploring the molecular mechanisms that underpin M. tuberculosis and dendritic cells interactions 
AWARDED BY: University of Southampton
DATE OF AWARD: 2024

DESCRIPTION OF THE DATA
This directory contains all the key data used to generate the thesis. It is organized by chapter, with subfolders grouped either by the experiment in which the data were used or by the figure number they support. Folder names are intended to clearly link the contents to the relevant experiment or figure. Where the link is not immediately clear, most folders containing multiple data files include a README file that provides additional context. Each README provides an overview of the data in that folder, the chapter it relates to, and the methods or sections used to generate it. 

This dataset contains:
> R scripts used for bulk RNA-seq, microarray and single cell RNA-seq analysis
> Flow cytometry .fcs and .wsp files used for monocyte purification, monocyte differentiation into MoDCs, quantifying HMOX1, PRNP, and TRFC protein expression, and BODIPY 581/591 C11 lipid peroxidation staining in HeLa cells and MoDCs
> RT-qPCR data RAW and analysed for gene expression in THP-1 cells and MoDCs
> All figure images - organised by Chapter
> .csv files containing lists of differentially expressed genes, gene ontology results and gene-gene co-expression
> Microscopy images of monocyte/MoDC differentiation and MoDC challenged with UV-killed M. tuberculosis

Date of data collection: Start - October/2019 End - March/2024

Licence:
CC BY

Related projects/Funders:
Medical Research Council - Funder

Date that the file was created: July/2025