ArticleNature structural & molecular biology2019
An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome.
Article in Nature structural & molecular biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 213 papers, 2 of them syntheses that pooled it.
What it found
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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.
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Who cites it
213 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Learning single-cell chromatin accessibility profiles using meta-analytic marker genes.Briefings in bioinformatics · 2023Pooled it
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
- Hybrid Encoding and Adaptive Guidance for Enhanced Single-Cell Multi-omics Clustering.Interdisciplinary sciences, computational life sciences · 2026Article
- Deep dynamical models of single-cell multiomic velocities predict loss-of-function and rescue perturbations in B cells.Nature biotechnology · 2026Article
- 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
- Decoding Skeletal Biology Through Transcriptomics: Insights from Bulk, Single-Cell, Spatial, and Multi-Omics Approaches.International journal of molecular sciences · 2026Review
- 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-cell ultra-high-throughput multiplexed chromatin accessibility and gene expression sequencing (SUM-seq).Nature protocols · 2026Review
- Article
- Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq.Nature protocols · 2026Review
- Deep dynamical models of single-cell multiomic velocities predict loss-of-function and rescue perturbations in B cells.bioRxiv : the preprint server for biology · 2026Article
- Conserved Transcriptional Circuits Regulate Cardiac Fibroblast-Mediated Fibrosis.Circulation research · 2026Article
- Article
- The molecular asynchrony of single cells.bioRxiv : the preprint server for biology · 2026Article
- Combined single-cell profiling of chromatin-transcriptome and splicing across brain cell types, regions and disease state.Nature biotechnology · 2026Article
- Quantifying Cross-Modal Association Confidence for Single-Cell RNA-ATAC Integration.bioRxiv : the preprint server for biology · 2026Article
- Article
- Early and late RNA eQTL are driven by different genetic mechanisms.Nature communications · 2026Article
- Benchmarking component choices for unpaired single cell RNA and epigenomic integration.Genome biology · 2026Article
153 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Simultaneous profiling of transcriptome and chromatin accessibility within single cells is a powerful approach to dissect gene regulatory programs in complex tissues. However, current tools are limited by modest throughput. We now describe an ultra high-throughput method, Paired-seq, for parallel analysis of transcriptome and accessible chromatin in millions of single cells. We demonstrate the utility of Paired-seq for analyzing the dynamic and cell-type-specific gene regulatory programs in complex tissues by applying it to mouse adult cerebral cortex and fetal forebrain. The joint profiles of a large number of single cells allowed us to deconvolute the transcriptome and open chromatin landscapes in the major cell types within these brain tissues, infer putative target genes of candidate enhancers, and reconstruct the trajectory of cellular lineages within the developing forebrain.
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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.