ArticleNature protocols2015
Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues.
Article in Nature protocols, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 306 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
306 citing papers in PubMed, 548 citations in OpenAlex.
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- Uncovering ectopic GC-like niches for tumor reactive lymphocyte priming in lung adenocarcinoma using Stereo-XCR-seq.Nature communications · 2026Article
- The applications of single-cell and spatial transcriptomics in neuroscience and brain disorders.Neuroscience and biobehavioral reviews · 2026Review
- Review
- Embryo-scale Visual Cell Sorting reveals a conserved transcriptomic signature of nucleolar size linked to proteostasis.bioRxiv : the preprint server for biology · 2026Article
- Review
- A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Spatially resolved in situ profiling of mRNA life cycle at transcriptome scale in intact cells and tissues using STARmap PLUS, RIBOmap and TEMPOmap.Nature protocols · 2026Review
- STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data.PLoS computational biology · 2026Article
- The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research.Genomics, proteomics & bioinformatics · 2026Review
- Programmable, target-induced fluorogenic CRISPR-tDeg platform for live-cell RNA visualization.Nucleic acids research · 2026Article
- Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications.Cancer cell · 2026Review
- Spider: a flexible and unified framework for simulating spatial transcriptomics data.Bioinformatics (Oxford, England) · 2026Article
- Applications and development of in situ nucleic acid visualization techniques.Frontiers in bioengineering and biotechnology · 2026Review
- Spatial omics and its applications for a tumour microenvironment characterization and precision medicine approach of gastric cancer.Ecancermedicalscience · 2026Review
- Spatial coherence in DNA barcode networks.Patterns (New York, N.Y.) · 2025Article
- ELLA: modeling subcellular spatial variation of gene expression within cells in high-resolution spatial transcriptomics.Nature communications · 2025Article
- STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data.bioRxiv : the preprint server for biology · 2025Article
- Profiling the heterogeneity of microbial populations and communities at the single-cell level.mLife · 2025Review
246 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
12 authors at 2 institutions in 1 country.
Funding
Abstract
RNA-sequencing (RNA-seq) measures the quantitative change in gene expression over the whole transcriptome, but it lacks spatial context. In contrast, in situ hybridization provides the location of gene expression, but only for a small number of genes. Here we detail a protocol for genome-wide profiling of gene expression in situ in fixed cells and tissues, in which RNA is converted into cross-linked cDNA amplicons and sequenced manually on a confocal microscope. Unlike traditional RNA-seq, our method enriches for context-specific transcripts over housekeeping and/or structural RNA, and it preserves the tissue architecture for RNA localization studies. Our protocol is written for researchers experienced in cell microscopy with minimal computing skills. Library construction and sequencing can be completed within 14 d, with image analysis requiring an additional 2 d.
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.