ArticleCell2018
Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH.
Article in Cell, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 203 papers.
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Who cites it
203 citing papers in PubMed.
- Integrative single-cell and spatial transcriptomic approaches to decipher the tumor microenvironment and therapeutic resistance in pancreatic cancer.Cancer biology & therapy · 2026Review
- Single-cell and spatial RNA sequencing in prostate cancer.Nature reviews. Urology · 2026Review
- Longitudinal live-cell chemical imaging using coherent Raman scattering microscopy.The Analyst · 2026Review
- Cohesin prevents local mixing of condensed euchromatic domains in living human cells.Nature genetics · 2026Article
- STAID: A Self-Refining Deep Learning Framework for Spatial Cell-Type Deconvolution with Biologically Informed Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The applications of single-cell and spatial transcriptomics in neuroscience and brain disorders.Neuroscience and biobehavioral reviews · 2026Review
- Transcription clusters and developmental pathways - nature, nurture, noise.Journal of cell science · 2026Review
- MicNet: integrating spatially resolved transcriptomes and pathology images by contrastive deep neural network.Genome biology · 2026Article
- Unprocessed U1 snRNAs as a biomarker of INTS11- and BRAT1-related neurodevelopmental disorders.Genome medicine · 2026Article
- SCUDDO: an unsupervised clustering algorithm for single-cell Hi-C maps using diagonal diffusion operators.Bioinformatics (Oxford, England) · 2026Article
- GatorST: A Versatile Contrastive Meta-Learning Framework for Spatial Transcriptomic Data Analysis.Small methods · 2026Article
- Beyond the Cell Atlas: Functional Communities as the Essential Pathologic Units Driving Kidney Disease.Journal of the American Society of Nephrology : JASN · 2026Review
- Whole-organism spatial transcriptomics at single-cell resolution inbioRxiv : the preprint server for biology · 2026Article
- Modern RNA Quantification Methods: From RT-qPCR to Advanced Microscopy.The journal of physical chemistry. B · 2026Review
- Cohesin prevents local mixing of condensed euchromatic domains in living human cells.bioRxiv : the preprint server for biology · 2026Article
- An experimentally-informed polymer model reveals high resolution organization of genomic loci.Nature communications · 2026Article
- Spatial mapping of RNA turnover kinetics and regulatory landscapes of mRNA stability in the mammalian brain.bioRxiv : the preprint server for biology · 2026Article
- Article
- 3D reconstruction of spatial transcriptomics with spatial pattern enhanced graph convolutional neural network.bioRxiv : the preprint server for biology · 2026Article
- S2potAE: multimodal spatial spot autoencoder integrating image and transcriptomic features for deconvolution.Briefings in bioinformatics · 2026Article
143 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
Abstract
Visualization of the transcriptome and the nuclear organization in situ has been challenging for single-cell analysis. Here, we demonstrate a multiplexed single-molecule in situ method, intron seqFISH, that allows imaging of 10,421 genes at their nascent transcription active sites in single cells, followed by mRNA and lncRNA seqFISH and immunofluorescence. This nascent transcriptome-profiling method can identify different cell types and states with mouse embryonic stem cells and fibroblasts. The nascent sites of RNA synthesis tend to be localized on the surfaces of chromosome territories, and their organization in individual cells is highly variable. Surprisingly, the global nascent transcription oscillated asynchronously in individual cells with a period of 2 hr in mouse embryonic stem cells, as well as in fibroblasts. Together, spatial genomics of the nascent transcriptome by intron seqFISH reveals nuclear organizational principles and fast dynamics in single cells that are otherwise obscured.
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