RNA sequencing articles from across Nature Portfolio

Spatial transcriptomics offers a glimpse of how microbiomes interact with their hosts.

Spatial transcriptomics (ST) enables gene expression characterisation within tissue sections, but comparing across sections and technologies remains challenging. Here, authors develop STalign to spatially align ST data and demonstrate applications including aligning to common coordinate frameworks.

Koelle and colleagues use an activation marker-dependent approach to determine the recruitment of TCR by three doses of mRNA vaccination in individuals previously infected with SARS-CoV-2.

Methodologies to study the mechanisms of cell–cell interactions in metastatic niches remain scarce. Here, the authors develop a secretory GFP reconstitution-based system to tag tissue-resident cells neighboring on cancer cells within the metastatic niche.

Computational deconvolution with single-cell RNA sequencing data as a reference is pivotal for interpreting spatial transcriptomics data. Here, authors present Redeconve, which improves the resolution by more than 100-fold with higher accuracy and speed.

DARLIN enables the generation of a massive diversity of barcodes for in vivo lineage tracing and the combination with single-cell multi-omics measurements.

Spatial transcriptomics offers a glimpse of how microbiomes interact with their hosts.

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.