README.md

Unraveling the Phenotypic States of Human innate-like T Cells: Comparative Insights with Conventional T Cells and Mouse Models

The thymus provides a unique and necessary environment for the proper development of T cells. While T cell development is deeply characterized in mouse models, there is still limited understanding of the development of T cells in the human thymus, more particularly for rarer T cell lineages such as iNKT, MAIT and γδ T cells, commonly referred to as innate-like T cells. Here, we used a combination of fluorescence-associated cell sorting, single-cell genomics and flow cytometry strategies in order to better understand commonalities and differences in the development of conventional and innate T cells in the human thymus, in addition to characterizing their molecular phenotype in the periphery.

This study is available as a preprint on bioRxiv. To explore the data interactively, you can use our ShinyCell app.

This repository contains all the scripts used to generate the figures contained in our manuscript. The repository to generate the interactive shiny app can be found here.

Software requirements

Data analysis and visualization was done in R version 4.1.3 and python version 3.8. Package versions were detailed in the methods section of the preprint. When necessary, specific scripts were run on an HPC cluster.

Directory structure

• scripts contains the final scripts that allow the (1) preprocessing of the data and (2) generation of figures in the manuscript;
• data_geo was created for the user to put the data files deposited on GEO;
• data_github contains small data files which were not uploaded on GEO (cNMF output files, gene signatures from the literature, etc.).