ArticleScience (New York, N.Y.)2015
Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.
Article in Science (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 770 papers.
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Who cites it
770 citing papers in PubMed.
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- A temporal single cell atlas of dynamic chromatin accessibility during murine lung maturation.Nature communications · 2026Article
- TopClust: Topological-based analysis of scRNA-seq data for data-driven identification of clusters and core cluster cells.Biophysical journal · 2026Article
- Somatic mosaicism in the brain: linking development, ageing and neurodegeneration.Nature reviews. Neurology · 2026Review
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- Deciphering global transcriptional dynamics coordinated by gene-gene regulatory interactions using single-cell data.Molecular systems biology · 2026Article
- Human body single-cell atlas of three-dimensional genome organization and DNA methylation.Science (New York, N.Y.) · 2026Article
- Unifying multimodal single-cell data with a mixture-of-expertsbioRxiv : the preprint server for biology · 2026Article
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- Reference Regulatory Element-Guided Gene Expression Analysis for Mechanistic Inference of Gene Regulatory Networks.bioRxiv : the preprint server for biology · 2026Article
- High-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequencing samples.Nature biotechnology · 2026Article
- Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq.Nature protocols · 2026Review
- Integrating Single-Cell Sequencing and Proteomics to Unravel Stem Cell Heterogeneity: Implications for Precision Regenerative Medicine.Stem cell reviews and reports · 2026Review
- Single-cell genomics links targeted functional manipulations to efficacy-associated chromatin signatures in CAR T cells.Research square · 2026Article
- scATAnno: Automated Cell Type Annotation for Single-cell ATAC-seq Data.Genomics, proteomics & bioinformatics · 2026Article
710 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
Abstract
Technical advances have enabled the collection of genome and transcriptome data sets with single-cell resolution. However, single-cell characterization of the epigenome has remained challenging. Furthermore, because cells must be physically separated before biochemical processing, conventional single-cell preparatory methods scale linearly. We applied combinatorial cellular indexing to measure chromatin accessibility in thousands of single cells per assay, circumventing the need for compartmentalization of individual cells. We report chromatin accessibility profiles from more than 15,000 single cells and use these data to cluster cells on the basis of chromatin accessibility landscapes. We identify modules of coordinately regulated chromatin accessibility at the level of single cells both between and within cell types, with a scalable method that may accelerate progress toward a human cell atlas.
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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.