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Deciphering heterogeneous populations of infecting bacteria with single-cell RNA-seq

Post-doc project The 'Excellence by Choice' postdoctoral project focuses on deciphering heterogeneous populations of infecting bacteria using single-cell RNA sequencing.

The project is financed by KAW.

Head of project

Project overview

Project period:

Start date: 2022-11-01

Participating departments and units at Umeå University

Department of Molecular Biology

Research area

Infection biology

External funding

Knut and Alice Wallenberg Foundation

Project description

Single-cell RNA sequencing has recently made strides that make it a powerful tool for detecting cellular heterogeneity in a variety of heterogeneous tissues or cell samples. 

In this study, we are using droplet microfluidics, one of the most promising high-throughput methods for quickly and effectively capturing and processing huge numbers of individual cells for whole-transcriptome or genomic analysis. However, we will encapsulate individual Yersinia pseudotuberculosis bacterial cells under T3SS in semi-permeable hydrogel microcapsules (SPCs) for single-cell analysis rather than employing droplets. Following encapsulation, the SPCs will house molecular biology procedures such as cell lysis, mRNA capture, cDNA synthesis and PCR, and barcoding employing barcoded oligos of the bacteria cell.

Finally, we will break the SPCs, demultiplex the cells, and utilize computational techniques to cluster the cells based on the different genes that are present in each cell. By doing so, we will be able to recognize the heterogeneity and sub-population associated with T3SS in Yersinia pseudotuberculosis thereby shedding light on bacterial infections. 

External funding

Latest update: 2023-10-10