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Semi-automated IT-scATAC-seq profiles cell-specific chromatin accessibility in differentiation and peripheral blood populations

Author

Listed:
  • Wei Jin

    (Guangdong Medical University
    Southern Medical University
    The University of Hong Kong)

  • Jingchun Ma

    (The University of Hong Kong)

  • Li Rong

    (The University of Hong Kong)

  • Shengshuo Huang

    (The University of Hong Kong)

  • Tuo Li

    (Changzheng Hospital)

  • Guoxiang Jin

    (Southern Medical University)

  • Zhongjun Zhou

    (Guangdong Medical University
    Southern Medical University
    The University of Hong Kong)

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.

Suggested Citation

  • Wei Jin & Jingchun Ma & Li Rong & Shengshuo Huang & Tuo Li & Guoxiang Jin & Zhongjun Zhou, 2025. "Semi-automated IT-scATAC-seq profiles cell-specific chromatin accessibility in differentiation and peripheral blood populations," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-57931-2
    DOI: 10.1038/s41467-025-57931-2
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    References listed on IDEAS

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