Abstract

Recent transcriptomic analyses allow to spatially resolve genome-wide gene expression in individual tissue sections at a subcompartment or near single-cell levels. In contrast to scRNA-seq, these emerging cutting-edge technologies conserve the footprint of the tissue structure in which the occurring cellular crosstalk dictates cell fates. The thymus that ensures the generation of a self-tolerant T-cell repertoire is composed of a large diversity of cell types (i.e. distinct stromal cells and developing T cells) that reciprocally control their respective differentiation. The main objective of this project is to determine in situ, using transgenic mouse models, the impact of developing T cells on the transcriptional programs governing the stromal cell heterogeneity. To this end, the candidate will use both commercially available solutions (e.g. 10X Genomics) and setup highly resolutive solutions (e.g. Slide-seq) to spatially study the thymic tissue transcriptome. Gene expression and spatial measurements will be combined to feed a model of complex cellular interplay.