Next-generation sequencing articles from across Nature Portfolio

While sequencing-based spatial transcriptomics has reached subcellular resolution, its low capture efficiency compromises downstream analysis. Here, authors present a spatial transcriptomic platform that achieves ~1μm resolution with substantially enhanced capture efficiency.

In this study, the authors benchmark four wastewater sequencing methods for influenza A, including two that were developed in-house. Using a custom probe panel they recover H1N1, H3N2, and H5N1, including H5N1 signals when dPCR was limited.

This protocol outlines multiplexed single-cell reduced-representation bisulfite sequencing (Msc-RRBS), a streamlined and scalable approach for parallel DNA methylation profiling of hundreds of individual cells.

A photolabile oligonucleotide system enables spatially resolved single-cell measurements to show how the epigenome regulates gene expression.

Metastatic breast cancer remains a heterogenous disease which is difficult to treat effectively. Here, the authors survey over 15,000 samples via cfDNA analysis and characterize the landscape of targetable alterations across major breast cancer subtypes.

SPAC-seq combines spatial transcriptomics and CRISPR screening within the tissue context, to identify how gene perturbations influence cell states and tissues.

In this Tools of the Trade article, Mariani (Bulyk Lab) describes the development of PIONEAR-Seq, a method designed to explore how genome composition influences transcription factor binding, particularly in the context of nucleosomes and other genomic elements.

Rapid identification of pathogenic viruses remains a critical challenge. A recent study advances this frontier by demonstrating a fully integrated memristor-based hardware system that accelerates genomic analysis by a factor of 51, while reducing energy consumption to just 0.2% of that required by conventional computational methods.

Epigenetic states are formed by the coordinated activity of several chromatin factors. Dam&ChIC recovers both past and current epigenetic states in single cells, revealing the timing and order of chromatin reorganization. It enabled us to identify how spatial chromatin localization is inherited upon mitosis, and to dissect successive chromatin remodeling events during the initiation of X-chromosome inactivation.

We introduce volumetric DNA microscopy, a technique that enables three-dimensional imaging of tissue morphology and gene expression in a single measurement. This feat is achieved by forming a huge intermolecular network of DNA barcodes within an intact specimen and encoding their pairwise proximities into a DNA sequence library.

In this Tools of the Trade article, Goronzy (Guttman lab) describes the development of ChIP-DIP, a high-throughput, split-pool barcoding method that enables genome-wide profiling of hundreds of regulatory proteins, transforming our ability to study the regulation of gene activity across cell types and biological contexts.