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Lapique, Kim, and colleagues present an open-source approach together with an online probe design platform for in situ RNA and protein analysis. This is an easy-to-use approach that enables vast feature detection, with cycling times under 20 minutes per feature.

Slide-seq profiling of mouse embryos at the onset of organogenesis (embryonic days 8.5–9.5) coupled with a new three-dimensional reconstruction and visualization tool (sc3D) provides high-resolution maps of spatiotemporal gene expression dynamics.

Nature Biotechnology asks a selection of faculty about the most exciting frontier in their field and the most needed technologies for advancing knowledge and applications.

Tangram is a versatile tool for aligning single-cell and single-nucleus RNA-seq data to spatially resolved transcriptomics data using deep learning.

The hypothalamic arcuate–median eminence (Arc-ME) complex is rich with functionally distinct cell types, a fraction of which have been characterized. The authors profile 20,921 individual cells by single-cell RNA-seq, identifying 50 Arc-ME cell types and their markers, determining each's response to energy status and implicating two neuron populations in the genetic control of obesity.

C-SIDE facilitates accurate cell type-specific differential expression analysis for multiple spatially resolved transcriptomics technologies by cell type mixture modeling.

Cell type mapping in spatial transcriptomics is enabled by accounting for compositional mixtures and differences in sequencing technologies.

Many perturbations affect only a subset of cells, while the rest remain largely unaffected. Existing single-cell analysis methods may fail to isolate the affected cells and their markers. Here, authors introduce HiDDEN, a machine learning method that reveals the perturbation status of individual cells.

The immune suppressive tumour microenvironment drives recurrence and metastatic disease in prostate cancer. Here authors provide a detailed analysis of the microenvironment via single cell RNA sequencing and high-resolution spatial transcriptomics to identify tumour-dependent changes compared to healthy tissue.

To construct a comprehensive atlas of cell types in each brain structure, we paired high-throughput single-nucleus RNA sequencing with Slide-seq, a recently developed spatial transcriptomics method with near-cellular resolution, across the entire mouse brain.

A technique using barcoded beads for DNA sequencing within tissue sections enables spatial resolution of tumour clonal heterogeneity and can be multiplexed with other analytical techniques for analysis of complex cellular phenotypes.

Spatial transcriptomics is enhanced by using imaging probes for subsets of genes.

A high-resolution kidney cellular atlas of 51 main cell types, including rare and previously undescribed cell populations, represents a comprehensive benchmark of cellular states, neighbourhoods, outcome-associated signatures and publicly available interactive visualizations.

Using single-cell RNA sequencing and spatial transcriptomics, Wang et al. recreate a map of glomerular locations in the mouse olfactory bulb. This work describes a spatial organization that may be used by the brain to assist in odor decoding.

Slide-tags enables multiomic sequencing of single cells and their localization within tissues.

An improved method for spatial transcriptomics with detection efficiency approaching that of droplet-based single-cell RNA-seq techniques.

Common polygenic variation at chromosome 16p and rare recurrent deletions of 16p11.2 influencing autism risk are associated with reduced expression of genes throughout the 16p region, suggesting functional convergence of rare and common variant effects.

We usually think of an individual's cells as sharing the same genome. Challenging this notion, two new studies show that somatic mosaicism is common and can be an early herald of cancer.

An imaging-free spatial transcriptomics method facilitates high-throughput barcode array generation up to centimeter scale.

Natural isolates of Caenorhabditis elegans nematodes differ in their sensitivity to the anti-exploratory pheromone icas#9, yielding two distinct foraging strategies that possess different survival advantages depending on environmental conditions such as food distribution.

Chen et al. find that cerebellar Purkinje cells directly inhibit neurons in parabrachial nuclei that in turn influence many forebrain regions. This alternative output pathway could enable the cerebellum to regulate emotions, anxiety, aggression and affect.

A comprehensive atlas of cell types and regional specializations in the mouse cerebellar cortex.

The authors show that graded molecular heterogeneity in metabotropic pathways underlies a continuum of temporal responses in cerebellar unipolar brush cells (UBCs). This allows the UBC population to serve as a cell-autonomous basis for temporal integration and learning over multiple time scales.

Marsh et al. demonstrate that enzymatic dissociation induces an aberrant ex vivo gene expression signature, most prominently in microglia, which when not addressed can substantially confound downstream analyses. They also identify a similar signature in postmortem human brain in snRNA-seq.

The authors used single-cell genomics to profile thousands of human dopamine neurons and identify one uniquely Parkinson’s disease-susceptible population, which was enriched for genetic risk for Parkinson’s disease.

Candelabrum cells have remained an obscure cerebellar cell type. The authors show that candelabrum cells are the most abundant Purkinje layer interneuron, are molecularly distinct and have a connectivity that allows them to control cerebellar output.

An examination of motor cortex in humans, marmosets and mice reveals a generally conserved cellular makeup that is likely to extend to many mammalian species, but also differences in gene expression, DNA methylation and chromatin state that lead to species-dependent specializations.

The authors describe an integrated atlas of the diverse cell types in the mouse primary motor cortex.

A single-cell atlas of the developing mouse cortex provides a temporal and spatial assessment of the molecular logic that drives the establishment and organization of cortical cell types.

The molecular circuitry that drives dendrite formation during osteocytogenesis remains poorly understood. Here the authors show that deletion of Sp7, a gene linked to rare and common skeletal disease, in mature osteoblasts and osteocytes causes severe defects in osteocyte dendrites.

Long-term cultures of human brain organoids display a high degree of cellular diversity, mature spontaneous neuronal networks and are sensitive to light.

Stevens and colleagues show that human stem-cell-differentiated microglia can be used to model the extensive transcriptional diversity of human brain microglia.

Nematodes socialize during feeding on bacteria; this behaviour depends on sophisticated integration of multiple sensory cues by a subset of the animal's 302 neurons. The RMG neurons are identified as the hub for such computations. Non-synaptic communication through 'gap junctions' is the key to RMG's regulation of neighbouring sensory neurons such as ASK (which responds to pheromones, a functional architecture that could be generalized to several other neuronal circuits).

SMART-seq3 reconstructs the full-length transcripts of single cells with high sensitivity.

High-quality multimodal single-cell, bulk and spatial genomics data are prepared from low-input, frozen needle biopsy specimens collected during routine clinical procedures.

This review provides an overview of analysis and experimental design of single-cell omics in the brain, emphasizing epigenomics and spatial omics. The authors discuss how the computational and experimental designs are interlinked, with both being guided by the biological questions.

The BRAIN Initiative Cell Census Network has constructed a multimodal cell census and atlas of the mammalian primary motor cortex in a landmark effort towards understanding brain cell-type diversity, neural circuit organization and brain function.

Spatial transcriptomics workflows, metrics and limitations are reviewed and discussed.

A new method tests whether disease heritability is enriched near genes with high tissue-specific expression. The authors use gene expression data together with GWAS summary statistics for 48 diseases and traits to identify disease-relevant tissues.

The Human BioMolecular Atlas Program (HuBMAP) presents its production phase: the generation of spatial maps of functional tissue units across organs from diverse populations and the creation of tools and infrastructure to advance biomedical research.

Here, the authors describe step-by-step procedures for integrating single-cell sequencing datasets from different experiments or modalities to identify common and distinct cell types using the R-based software tool LIGER.

The vertebrate-conserved and germline-specific RNA-binding protein DND1 recruits the CCR4–NOT deadenylase complex to destabilize its mRNA targets and is required for the maintenance of germline stem cells.