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A rapid and robust method for single cell chromatin accessibility profiling

Author

Listed:
  • Xi Chen

    (Wellcome Sanger Institute)

  • Ricardo J. Miragaia

    (Wellcome Sanger Institute
    MedImmune)

  • Kedar Nath Natarajan

    (Wellcome Sanger Institute
    Functional Biology and Metabolism Unit, Biochemistry and Molecular Biology, SDU)

  • Sarah A. Teichmann

    (Wellcome Sanger Institute
    EMBL-European Bioinformatics Institute
    Theory of Condensed Matter, Cavendish Laboratory)

Abstract

The assay for transposase-accessible chromatin using sequencing (ATAC-seq) is widely used to identify regulatory regions throughout the genome. However, very few studies have been performed at the single cell level (scATAC-seq) due to technical challenges. Here we developed a simple and robust plate-based scATAC-seq method, combining upfront bulk Tn5 tagging with single-nuclei sorting. We demonstrate that our method works robustly across various systems, including fresh and cryopreserved cells from primary tissues. By profiling over 3000 splenocytes, we identify distinct immune cell types and reveal cell type-specific regulatory regions and related transcription factors.

Suggested Citation

  • Xi Chen & Ricardo J. Miragaia & Kedar Nath Natarajan & Sarah A. Teichmann, 2018. "A rapid and robust method for single cell chromatin accessibility profiling," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-07771-0
    DOI: 10.1038/s41467-018-07771-0
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    Cited by:

    1. Jules Samaran & Gabriel Peyré & Laura Cantini, 2024. "scConfluence: single-cell diagonal integration with regularized Inverse Optimal Transport on weakly connected features," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    2. Maria Stahl Madsen & Marjoleine F. Broekema & Martin Rønn Madsen & Arjen Koppen & Anouska Borgman & Cathrin Gräwe & Elisabeth G. K. Thomsen & Denise Westland & Mariette E. G. Kranendonk & Marian Groot, 2022. "PPARγ lipodystrophy mutants reveal intermolecular interactions required for enhancer activation," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    3. Shaghayegh Nouruzi & Dwaipayan Ganguli & Nakisa Tabrizian & Maxim Kobelev & Olena Sivak & Takeshi Namekawa & Daksh Thaper & Sylvan C. Baca & Matthew L. Freedman & Adeleke Aguda & Alastair Davies & Ami, 2022. "ASCL1 activates neuronal stem cell-like lineage programming through remodeling of the chromatin landscape in prostate cancer," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    4. Javier Rodríguez-Ubreva & Anna Arutyunyan & Marc Jan Bonder & Lucía Del Pino-Molina & Stephen J. Clark & Carlos de la Calle-Fabregat & Luz Garcia-Alonso & Louis-François Handfield & Laura Ciudad & Edu, 2022. "Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responses," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    5. Kai Cao & Qiyu Gong & Yiguang Hong & Lin Wan, 2022. "A unified computational framework for single-cell data integration with optimal transport," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    6. Ziqi Zhang & Haoran Sun & Ragunathan Mariappan & Xi Chen & Xinyu Chen & Mika S. Jain & Mirjana Efremova & Sarah A. Teichmann & Vaibhav Rajan & Xiuwei Zhang, 2023. "scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

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