ArticleNature protocols2021
Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2).
Article in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 1 of them a synthesis that pooled it.
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Who cites it
38 citing papers in PubMed, 1 synthesis or guideline pooled it, 47 citations in OpenAlex.
- Graph neural networks for single-cell omics data: a review of approaches and applications.Briefings in bioinformatics · 2025Pooled it
- 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
- CTCF aligns single-cell TAD-like domain boundaries and stabilizes long-range active chromatin clusters.Science advances · 2026Article
- mmVelo: a deep generative model for estimating cell state-dependent dynamics across multiple modalities.Bioinformatics (Oxford, England) · 2026Article
- Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq.Nature protocols · 2026Review
- Beyond the Cell Atlas: Functional Communities as the Essential Pathologic Units Driving Kidney Disease.Journal of the American Society of Nephrology : JASN · 2026Review
- Exploring single-cell and multi-omics technologies and their role in unraveling tumor heterogeneity of hepatocellular carcinoma.Journal of liver cancer · 2026Review
- Dissecting Normal and Abnormal Human Kidney Development Using Multiomics.Journal of the American Society of Nephrology : JASN · 2026Review
- Enhancer Dynamics for Gene Regulation in the Cardiovascular System.Arteriosclerosis, thrombosis, and vascular biology · 2026Review
- Single-cell multiomic human brain atlas reveals regulatory drivers of cortical regionality.Nature communications · 2026Article
- Advances in scCUT&Tag and computational analysis for single-cell gene regulatory element mapping.Briefings in bioinformatics · 2026Review
- Review
- Single-cell epigenomics and proteomics methods integrated in multiomics.Fundamental research · 2025Review
- Single-cell multi-omics in cancer immunotherapy: from tumor heterogeneity to personalized precision treatment.Molecular cancer · 2025Review
- Deciphering gene regulatory programs in mouse embryonic skin through single-cell multiomics analysis.Genome biology · 2025Article
- A Multimodal Spatial and Epigenomic Atlas of Human Adult Lung Topography.bioRxiv : the preprint server for biology · 2025Article
- Combining single-cell ATAC and RNA sequencing for supervised cell annotation.BMC bioinformatics · 2025Article
- Single-Cell Analysis in the Mouse and Human Mammary Gland.Advances in experimental medicine and biology · 2025Review
- Implementing distinct spatial proteogenomic technologies: opportunities, challenges, and key considerations.Clinical and experimental immunology · 2024Review
- GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells.Nature genetics · 2024Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
Abstract
Comprehensive characterization of cellular heterogeneity and the underlying regulatory landscapes of tissues and organs requires a highly robust and scalable method to acquire matched RNA and chromatin accessibility profiles on the same cells. Here, we describe a single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2) assay, implemented with cellular combinatorial indexing. This method involves tagmentation within permeabilized and fixed single-nucleus isolates to capture accessible chromatin (AC) regions, followed by the capture and reverse transcription of RNA transcripts. Through combinatorial split pool ligations, cDNA and AC within each single nucleus become appended with a common cell barcode combination. The captured cDNA and AC are then co-amplified before splitting and enrichment into single-nucleus RNA and single-nucleus AC sequencing libraries. This protocol is compatible with both nuclei and whole cells and can be completed in 3.5 d. SNARE-seq2 permits robust generation of high-quality, joint single-cell RNA and AC sequencing libraries from hundreds of thousands of single cells per experiment.
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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.