ArticleNature communications2025
Semi-automated IT-scATAC-seq profiles cell-specific chromatin accessibility in differentiation and peripheral blood populations.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- scATAnno: Automated Cell Type Annotation for Single-cell ATAC-seq Data.Genomics, proteomics & bioinformatics · 2026Article
- Cell type annotation for scATAC-seq via DNA large language model and graph domain adaptation.PLoS computational biology · 2026Article
- IT-scC&T-seq streamlines scalable, parallel profiling of protein-DNA interactions in single cells.Genome biology · 2025Article
- Cell-Type Annotation for scATAC-Seq Data by Integrating Chromatin Accessibility and Genome Sequence.Biomolecules · 2025Article
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Authors and funding
7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Single-cell ATAC-seq (scATAC-seq) enables high-resolution mapping of chromatin accessibility but is often limited by throughput, cost, and equipment requirements. Here, we present indexed Tn5 tagmentation-based scATAC-seq (IT-scATAC-seq), a semi-automated, cost-effective, and scalable approach that leverages indexed Tn5 transposomes and a three-round barcoding strategy. This workflow prepares libraries for up to 10,000 cells in a single day, reduces the per-cell cost to approximately $0.01, and maintains high data quality. Comprehensive benchmarking demonstrates that IT-scATAC-seq achieves robust library complexity, high signal specificity, and improved cost-efficiency compared to existing methods. We apply IT-scATAC-seq to mouse embryonic stem cells, capturing chromatin remodelling during early differentiation, and to human peripheral blood mononuclear cells, resolving cell-type-specific regulatory programs. Here, we show that IT-scATAC-seq provides a robust and efficient approach for high-resolution single-cell epigenomic investigations, balancing scalability, data quality, and accessibility.
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Registered trials
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