ArticleNature communications2023
Spatial Transcriptomics-correlated Electron Microscopy maps transcriptional and ultrastructural responses to brain injury.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
45 citing papers in PubMed, 59 citations in OpenAlex.
- Transcriptomic landscape of microglia in mouse models of social dysfunction and oxytocin-mediated recovery.iScience · 2026Article
- Islet ultrastructure: past achievements and future directions.Diabetologia · 2026Review
- Single-cell insights into plant growth, adaptation, and evolution.Journal of integrative plant biology · 2026Review
- Foamy microglia link oxylipins to disease progression in multiple sclerosis.Nature neuroscience · 2026Article
- The applications of single-cell and spatial transcriptomics in neuroscience and brain disorders.Neuroscience and biobehavioral reviews · 2026Review
- Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets.Nature biotechnology · 2026Article
- Gpnmb defines a phagocytic state of microglia linked to cell death in prion disease mouse model.Nature communications · 2026Article
- STORM: spatial transcriptomics optimization by resolution via matrix factorization.Briefings in bioinformatics · 2026Article
- MISSTE: a multiscale integrative spatial simulator for understanding the mechanisms underlying tissue ecosystems.bioRxiv : the preprint server for biology · 2026Article
- Simultaneous spatial transcriptomics and morphology profiling as tools to explore how microglia change with age.Nature aging · 2026Article
- In vivo CRISPR screen reveals regulation of macrophage states in neuroinflammation.Nature neuroscience · 2026Article
- Peroxisomal integrity in demyelination-associated microglia enables cellular debris clearance and myelin renewal in mice.The Journal of clinical investigation · 2026Article
- Article
- SpatialProp: tissue perturbation modeling with spatially resolved single-cell transcriptomics.bioRxiv : the preprint server for biology · 2025Article
- Review
- Single-nucleus profiling highlights the all-brain echinoderm nervous system.Science advances · 2025Article
- Article
- Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem.Nature methods · 2025Article
- Microglia networks within the tapestry of alzheimer's disease through spatial transcriptomics.Molecular neurodegeneration · 2025Review
- A comprehensive comparison on clustering methods for multi-slice spatially resolved transcriptomics data analysis.Briefings in bioinformatics · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the complexity of cellular function within a tissue necessitates the combination of multiple phenotypic readouts. Here, we developed a method that links spatially-resolved gene expression of single cells with their ultrastructural morphology by integrating multiplexed error-robust fluorescence in situ hybridization (MERFISH) and large area volume electron microscopy (EM) on adjacent tissue sections. Using this method, we characterized in situ ultrastructural and transcriptional responses of glial cells and infiltrating T-cells after demyelinating brain injury in male mice. We identified a population of lipid-loaded "foamy" microglia located in the center of remyelinating lesion, as well as rare interferon-responsive microglia, oligodendrocytes, and astrocytes that co-localized with T-cells. We validated our findings using immunocytochemistry and lipid staining-coupled single-cell RNA sequencing. Finally, by integrating these datasets, we detected correlations between full-transcriptome gene expression and ultrastructural features of microglia. Our results offer an integrative view of the spatial, ultrastructural, and transcriptional reorganization of single cells after demyelinating brain injury.
Indexed as
Identifiers
What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.