ArticleScience (New York, N.Y.)2014
Highly multiplexed subcellular RNA sequencing in situ.
Article in Science (New York, N.Y.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 556 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
556 citing papers in PubMed, 1 synthesis or guideline pooled it, 1,005 citations in OpenAlex.
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
- Spatiotemporal Resolution for Neurodegenerative Diseases: Linking Proteinopathy, Cellular Vulnerability, and Disease Trajectories.Neuroscience bulletin · 2026Review
- 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
- Deep Learning-Assisted Prioritization of Candidate Drug Targets in Tumors Using Spatial Multi-Omics.Biology · 2026Review
- Article
- Advances in single-cell and spatial multi-omics for plant development and stress responses.Plant diversity · 2026Review
- Artificial intelligence in spatial transcriptomics: a review of methods, datasets, and directions.Briefings in bioinformatics · 2026Review
- Volumetric DNA microscopy for mapping spatial transcriptomes in three dimensions.Nature protocols · 2026Review
- Transforming subcellular spatial transcriptomics: deep learning models for cell segmentation.Nucleic acids research · 2026Review
- APEX-seq maps transcriptome-wide subcellular RNA localization in living cells.Nature protocols · 2026Review
- Tissue and cellular spatiotemporal dynamics in colon aging.Nature biotechnology · 2026Article
- Toward simultaneous pseudo-space reconstruction and cell-type deconvolution of single-cell spatial transcriptome using SpaDicer.Cell reports methods · 2026Article
- Spatial Transcriptomics for Dissecting Cellular and Molecular Heterogeneity in the Aging and Diseased Brain.International journal of molecular sciences · 2026Review
- Dissecting human organ development using spatial technologies.Developmental cell · 2026Review
- MCFST: spatial domain identification method based on multi-view graph convolutional network and graph fusion network.Bioinformatics (Oxford, England) · 2026Article
- Spatially tunable multiomic sequencing using light-driven combinatorial barcoding of molecules in tissues.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Logistic regression for estimating functional effects with spatial transcriptomics.Nucleic acids research · 2026Article
496 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
19 authors at 2 institutions in 1 country.
Funding
Abstract
Understanding the spatial organization of gene expression with single-nucleotide resolution requires localizing the sequences of expressed RNA transcripts within a cell in situ. Here, we describe fluorescent in situ RNA sequencing (FISSEQ), in which stably cross-linked complementary DNA (cDNA) amplicons are sequenced within a biological sample. Using 30-base reads from 8102 genes in situ, we examined RNA expression and localization in human primary fibroblasts with a simulated wound-healing assay. FISSEQ is compatible with tissue sections and whole-mount embryos and reduces the limitations of optical resolution and noisy signals on single-molecule detection. Our platform enables massively parallel detection of genetic elements, including gene transcripts and molecular barcodes, and can be used to investigate cellular phenotype, gene regulation, and environment in situ.
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.