ArticleNature communications2023
Spatial organization of the mouse retina at single cell resolution by MERFISH.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 52 papers, 1 of them a synthesis that pooled it.
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
52 citing papers in PubMed, 1 synthesis or guideline pooled it, 60 citations in OpenAlex.
- Enhancing RNA Capture Efficiency in Spatial Transcriptomics: A Review of Innovative Technologies and Strategies.International journal of molecular sciences · 2025Pooled it
- Unveiling the role of spatial transcriptomics in the analysis of the tumor immune microenvironment (Review).International journal of molecular medicine · 2026Review
- Conservation of retinal direction-selective circuits across vertebrate species.Current opinion in genetics & development · 2026Review
- The extreme diversity of retinal amacrine cells has deep evolutionary roots.Science advances · 2026Article
- Single-Cell Annotation and Localization via Integrating Spatial Transcriptomics Maps the Mouse Ocular Atlas and RAO Dynamics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Understanding nerve-tumor interactions: From basic biology to therapeutic innovation.Genes & diseases · 2026Review
- SMURF: soft-segmentation for single-cell reconstruction and topological analysis of spatial transcriptomic data.Nature communications · 2026Article
- An Integrated muti-omics cell atlas of the human trabecular meshwork and ciliary body.bioRxiv : the preprint server for biology · 2026Article
- Single-cell and spatial transcriptomic analyses of gene therapy-associated retinal inflammation in non-human primates.Molecular therapy. Advances · 2026Article
- Spatiotemporal cell type deconvolution leveraging tissue structure.Research square · 2026Article
- Paired DNA and RNA sequencing uncovers common and rare variation regulating human retinal gene expression.Nature communications · 2026Article
- The Extreme Diversity Of Retinal Amacrine Cells Has Deep Evolutionary Roots.bioRxiv : the preprint server for biology · 2026Article
- Review
- Spatiotemporal cell type deconvolution leveraging tissue structure.bioRxiv : the preprint server for biology · 2026Article
- Systematic discovery of retina-enriched Rik genes identifies 1190005I06Rik as a novel modulator of visual signalling.Journal of translational medicine · 2026Article
- Synaptic control of retinal ganglion cell survival and axon regeneration.Molecular neurodegeneration · 2026Review
- Applications and development of in situ nucleic acid visualization techniques.Frontiers in bioengineering and biotechnology · 2026Review
- The CD39-CD73-adenosine axis: a pivotal regulator of retinal homeostasis and diseases.Frontiers in cell and developmental biology · 2026Review
- Intravitreal exposure to the SARS-CoV-2 spike protein is associated with aggravated retinal lesions in a murine model of central retinal vein occlusion.Frontiers in medicine · 2026Article
- Spatial transcriptomics reveals injury-responsive compartments and coordinated immune-fibrotic signaling in ANCA-associated renal vasculitis.Frontiers in immunology · 2026Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The visual signal processing in the retina requires the precise organization of diverse neuronal types working in concert. While single-cell omics studies have identified more than 120 different neuronal subtypes in the mouse retina, little is known about their spatial organization. Here, we generated the single-cell spatial atlas of the mouse retina using multiplexed error-robust fluorescence in situ hybridization (MERFISH). We profiled over 390,000 cells and identified all major cell types and nearly all subtypes through the integration with reference single-cell RNA sequencing (scRNA-seq) data. Our spatial atlas allowed simultaneous examination of nearly all cell subtypes in the retina, revealing 8 previously unknown displaced amacrine cell subtypes and establishing the connection between the molecular classification of many cell subtypes and their spatial arrangement. Furthermore, we identified spatially dependent differential gene expression between subtypes, suggesting the possibility of functional tuning of neuronal types based on location.
Indexed as
Identifiers
What OpenQuestion 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 OpenQuestion graph.