Design

The idea behind the work of the transcriptomics group is to try and detect any changes in the gene expression when E. coli is grown alongside strongyles as opposed to just being grown in a normal lab environment. The aim for this undertaking is to find any and all genes which might be expressed exclusively in the proximity to the worms - giving us a prime opportunity to work some biotech magic and find a way to make a diagnostics tool for the strongyle parasites out of that very bacteria gene.

The way we decided to approach this was by running a full-scale transcriptome sequencing on the entire E. coli genome, both in bacteria grown normally and grown alongside the worms. By doing this, we would be able to quantitatively determine the differences in gene expression.

For this, we created an eight-step pipeline starting from lysing the bacteria to extracting their RNA contents, to refining and finally sequencing the genetic material using Oxford Nanopore’s MinION device - which you plug in to your laptop. That same laptop will then be used to understand what exactly is going on in the bacteria.