Method-dependent biases in cell type detection between single-cell and single-nucleus RNA sequencing in the photosymbiotic acoel Praesagittifera naikaiensis
Background Comparisons of single-cell and single-nucleus RNA sequencing (scRNA-seq and snRNA-seq) data have been described in some mammalian tissues and, subsequently, in Drosophila, but remain unexplored in most invertebrate lineages. The xenacoelomorphs occupy key phylogenetic positions, yet they differ anatomically from mammals. They have a reduced extracellular matrix, high-salt body fluid,…
In a recent study comparing single-cell and single-nucleus RNA sequencing (scRNA-seq and snRNA-seq) in the photosymbiotic acoel Praesagittifera naikaiensis, researchers found significant method-dependent biases. Both techniques produced high-quality data with comparable gene detection, but scRNA-seq captured a larger proportion of symbiotic algae RNA.
Neural genes were enriched in snRNA-seq, while snRNA-seq recovered several cell populations underrepresented in scRNA-seq, including muscle and metabolically active clusters. Cross-method label transfer and integration-based validation identified six snRNA-seq clusters with no clear scRNA-seq counterpart. Despite these technical differences, neural transcript recovery in snRNA-seq was consistent with previous mammalian studies, and snRNA-seq proved beneficial for cell atlas construction in non-model, symbiotic invertebrates.
Written by urgent.news from bioRxiv's reporting — not their text. Machine-written — may contain errors; check the original before relying on it.
