Dan Turner leads the Applications Team at Oxford Nanopore Technologies and presented at London Calling 2022 a session entitled “A single platform for multi-omics.” Turner mentioned that they have developed a set of posters for different applications. They spoke about epithelial to mesenchymal transition (EMT). They are able to analyze this process using Nanopore sequencing and various data types. Turner explained that they are interested in this process because it is involved in development and cancer. They described mesenchymal cells as multipotent stromal cells. These cells can also invade tissues. Interestingly, these cells can also change back from cancerous to epithelial cells. Turner explained their experiment. They began with mesenchymal cells and extracted DNA and RNA as they induced growth of these cells. For bulk transcriptomics they determined gene expression and discovered isoforms. cDNA sequencing can be done over the time course of the experiment. Turner said the kit can be used for quantitative analyses of expression. They said gene-level information is useful but you can “zoom in” to learn about isoforms. For single-cell transcriptomics, they used a “split-seq” system in which you pool, split, and include a barcode. The idea is that there is “little chance that any two cells will have the same barcode because there are so many barcodes.” Expression of genes can be monitored by day. The next level is to analyze isoforms per cell, and Turner noted that they have that data and have analyzed it. Next, Turner explained how they used Pore-C to look at long-range, 3-dimensional genome interactions. Pore-C can be used to investigate long-range interactions using Nanopore sequencing. Turner shared a graph of genome organization by sequence and from interaction data. The plot was a diagonal with some outliers. Next, Turner talked about bulk DNA sequencing and detection of methylation. They explained how Nanopore sequencing can be used to detection structural variations and phase based on methylation patterns. The long reads also help identify deletions. Turner explained that some deletions occur in regions differentially methylated. Thus, they used adaptive sampling and a custom BED file to sequence those regions. The ability to use one platform for multi-omics is really powerful and highlighted with this series of experiments and approaches.
