Gene expression analysis articles from across Nature Portfolio

Using multiplexed spatially resolved transcriptomic approaches, the authors generate a topographic atlas of the healthy adult lung with location-related gene expression variability or neighbourhood changes as exemplified by COPD patient sample analysis.

Chan et al. generate a high-resolution spatiotemporal atlas of healing hearts and reveal cellular networks of lesion repair, including macrophage–fibroblast interactions that control late-stage fibrosis and immune niches that induce cardiomyocyte de-differentiation.

The 64-plex fluorescence imaging of RNA in tissues is achieved in one imaging cycle

Jean Fan recounts a 2015 paper by Martincorena et al. that revealed oncogenic mutations in normal tissues, also highlighting how the latest spatial technologies can now be used to study the spatial contextual impact of these mutations.

The effector fates of innate lymphoid cells (ILCs) are epigenetically imprinted early in ontogeny through the selective loss of DNA methylation at signature genes encoding fate-determining regulators — a process that is important for functional diversification of barrier immunity.

Now a protocol enables simultaneous measurement of gene expression and chromatin state in intact tissues, unlocking the relationship between tissue architecture and gene regulation.

In this Journal Club, Shila Ghazanfar highlights a seminal paper by Levsky et al. that paved the way for contemporary single-cell spatial transcriptomics.

This Comment discusses the progress, limitations and best practices in applying foundation models to single-cell omics data.