ArticleNature methods2022
ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells.
Article in Nature methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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72 citing papers in PubMed, 105 citations in OpenAlex.
- DUET-seq: An Open-Source Droplet Platform for High-Fidelity Joint Chromatin and Transcriptome Profiling Reveals Temporal Regulatory Decoupling in Single Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Continual integration of single-cell multimodal data with MIRACLE.Nature computational science · 2026Article
- mmVelo: a deep generative model for estimating cell state-dependent dynamics across multiple modalities.Bioinformatics (Oxford, England) · 2026Article
- Mapping enhancer-gene regulatory interactions from single-cell data.Nature genetics · 2026Article
- Single-cell ultra-high-throughput multiplexed chromatin accessibility and gene expression sequencing (SUM-seq).Nature protocols · 2026Review
- Graph-based contrastive learning enables unified integration and niche transfer across single-cell and spatial multi-omics.Briefings in bioinformatics · 2026Article
- Convergence of schizophrenia risk genes on CALN1 disrupts human forebrain development and drives core psychotic behaviors including hallucination-like perception.BMC medicine · 2026Article
- Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq.Nature protocols · 2026Review
- A Simple, Cost-Effective, High-Throughput Method for Measuring Chromatin Accessibility and Gene Expression in Single Nuclei.bioRxiv : the preprint server for biology · 2026Article
- The molecular asynchrony of single cells.bioRxiv : the preprint server for biology · 2026Article
- Article
- Distinguishing causal from tagging enhancers using single-cell multiome data.medRxiv : the preprint server for health sciences · 2026Article
- Single-Cell and Spatial Multi-Omics in Small-Intestinal Homeostasis and Ischemia/Reperfusion Injury: Current Advances, Applications, and Future Perspectives.Journal of inflammation research · 2026Review
- Computational Analyses and Challenges of Single-cell ATAC-seq.Genomics, proteomics & bioinformatics · 2025Review
- multiVIB: A unified probabilistic contrastive learning framework for atlas-scale integration of single-cell multi-omics data.bioRxiv : the preprint server for biology · 2025Article
- Kidney diseases and single-cell sequencing research: a bibliometric analysis from 2015 to 2024.Renal failure · 2025Review
- The applications of single-cell multiomics in drug screening.Pharmaceutical science advances · 2025Review
- Review
- scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples.Nature communications · 2025Article
- Assessment and applications of joint profiling of single-cell chromatin accessibility and transcriptome.Briefings in bioinformatics · 2025Review
12 more citing papers are in PubMed but not listed here.
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11 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Joint profiling of chromatin accessibility and gene expression from the same single cell provides critical information about cell types in a tissue and cell states during a dynamic process. Here, we develop in situ sequencing hetero RNA-DNA-hybrid after assay for transposase-accessible chromatin-sequencing (ISSAAC-seq), a highly sensitive and flexible single-cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single nucleus. We demonstrated that ISSAAC-seq is sensitive and provides high quality data with orders of magnitude more features than existing methods. Using the joint profiles from over 10,000 nuclei from the mouse cerebral cortex, we uncovered major and rare cell types and cell-type specific regulatory elements and identified heterogeneity at the chromatin level within established cell types defined by gene expression. Finally, we revealed distinct dynamics and relationships of gene expression and chromatin accessibility during an oligodendrocyte maturation trajectory.
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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.