Optimisation of single-nuclei isolation and RNA sequencing of parasitic nematodes

Abstract

Single-cell/nuclei transcriptomics has revolutionised our understanding of cell, tissue, and organismal biology during health and disease of humans and model organisms. However, for non-model species, reassessment and refinement of conventional methods to address novel technical and biological challenges are needed. Here, we evaluate three established nuclei isolation protocols and, building on our experiences, optimised single nuclei isolation for parasitic nematodes (SNIP). We test the versatility of our SNIP protocol on evolutionarily and morphologically distinct species and life stages and validate by snRNA-seq to reveal sex, stage, and tissue-specific gene expression. Optimised protocols will advance the understanding of parasitic nematodes, from fundamental biology to infection and disease.