ArticleCell2021
Microscopic examination of spatial transcriptome using Seq-Scope.
Article in Cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 305 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
305 citing papers in PubMed, 1 synthesis or guideline pooled it, 531 citations in OpenAlex.
- Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective.Briefings in bioinformatics · 2025Pooled it
- Spatial Transcriptomics Analysis of Ewing Sarcoma.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Integrative single-cell and spatial transcriptomic approaches to decipher the tumor microenvironment and therapeutic resistance in pancreatic cancer.Cancer biology & therapy · 2026Review
- Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward.The Plant cell · 2026Review
- Spatial chromatin architecture and accessibility co-profiling of mammalian tissues.Nature methods · 2026Article
- Resolving cell-cell interaction networks and their molecular logic in complex tissues.Nature methods · 2026Article
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Insights Into Spatial Transcriptomics: Exploring Recent Technical Developments and Their Diverse Applications.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Review
- Mapping Embryonic Mouse Lung Development Using Enhanced Spatial Transcriptomics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Photolabile oligonucleotides with topological light gradients enable spatially resolved single-cell transcriptomics and epigenomics.Nature biotechnology · 2026Article
- HIGH-DIMENSIONAL MULTI-OMIC MAPPING OF POST-MORTEM HUMAN BRAIN USING ITERATIVE INDIRECT IMMUNOFLUORESCENCE IMAGING ON XENIUM-PROCESSED TISSUES.bioRxiv : the preprint server for biology · 2026Article
- Ten quick tips for spatial transcriptomics analysis.PLoS computational biology · 2026Review
- Amplification bias in sequencing-based spatial transcriptomics: sources, mechanisms, impacts, and mitigation strategies.Briefings in bioinformatics · 2026Review
- Highly Sensitive Spatial Host-Microbiome Transcriptomics in FFPE Tissues via Iterative Hydrogel Expansion.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- PRISM: Prior-enhanced Inference for Spatial Transcriptomic Cell Type Mapping.Bioinformatics (Oxford, England) · 2026Article
- Tools and tactics for studying alternative splicing.Nature reviews. Genetics · 2026Review
- Insights into programmed cell death from multiple imaging modalities.Journal of translational medicine · 2026Review
- Dissecting human organ development using spatial technologies.Developmental cell · 2026Review
- Graph-based contrastive learning enables unified integration and niche transfer across single-cell and spatial multi-omics.Briefings in bioinformatics · 2026Article
245 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
Spatial barcoding technologies have the potential to reveal histological details of transcriptomic profiles; however, they are currently limited by their low resolution. Here, we report Seq-Scope, a spatial barcoding technology with a resolution comparable to an optical microscope. Seq-Scope is based on a solid-phase amplification of randomly barcoded single-molecule oligonucleotides using an Illumina sequencing platform. The resulting clusters annotated with spatial coordinates are processed to expose RNA-capture moiety. These RNA-capturing barcoded clusters define the pixels of Seq-Scope that are ∼0.5-0.8 μm apart from each other. From tissue sections, Seq-Scope visualizes spatial transcriptome heterogeneity at multiple histological scales, including tissue zonation according to the portal-central (liver), crypt-surface (colon) and inflammation-fibrosis (injured liver) axes, cellular components including single-cell types and subtypes, and subcellular architectures of nucleus and cytoplasm. Seq-Scope is quick, straightforward, precise, and easy-to-implement and makes spatial single-cell analysis accessible to a wide group of biomedical researchers.
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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.