RNA sequencing articles from across Nature Portfolio

In situ spatial transcriptomic analysis of more than 1 million cells are used to create a 200-nm-resolution spatial molecular atlas of the adult mouse central nervous system and identify previously unknown tissue architectures.

capTEs is a long-read targeted RNA-sequencing method that can quantify the expression of reference and non-reference transposable elements at the level of genomic loci.

mRNA vaccines must be rigorously analysed to measure their integrity and detect contaminants, which can be time-consuming and costly. Here, authors describe a method to analyse mRNA vaccine quality using long-read sequencing and a custom bioinformatic pipeline.

A paper in Science reports a time-resolved multiomic atlas of the human yolk sac, expanding knowledge of this poorly resolved structure in humans.

Ribosome-bound mRNA mapping (RIBOmap) enables three-dimensional in situ detection of spatially resolved protein synthesis in single cells.

A decade ago, the first bioinformatics pipelines to detect circular RNA molecules based on short-read sequencing data were published. Here, we show that dozens of such circular RNA detection tools differ vastly in their sensitivity but not in their specificity.

In this Tools of the Trade article, Christa Haase (at the Charles Lin lab) describes a technique called Image-seq that enables image-guided cell isolation from a specific, intact tissue location for subsequent single-cell gene expression analysis.

A study in Nature Biotechnology describes Scriabin, a highly scalable framework for inference of cell–cell communication from scRNA-seq data at the level of individual cells.

By conducting single-cell meta-analyses of inflammatory bowel disease, we identify rare or less-characterized cell subtypes linked to GWAS risk genes and therapeutic targets and dissect the commonalities and differences between ulcerative colitis and Crohn’s disease. Consequently, we present an interactive and user-friendly platform for the research community.