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Single cell dual-omic atlas of the human developing retina

Author

Listed:
  • Zhen Zuo

    (Baylor College of Medicine
    Baylor College of Medicine)

  • Xuesen Cheng

    (Baylor College of Medicine)

  • Salma Ferdous

    (Baylor College of Medicine)

  • Jianming Shao

    (Baylor College of Medicine)

  • Jin Li

    (Baylor College of Medicine)

  • Yourong Bao

    (Baylor College of Medicine)

  • Jean Li

    (Baylor College of Medicine)

  • Jiaxiong Lu

    (Baylor College of Medicine)

  • Antonio Jacobo Lopez

    (Sacramento)

  • Juliette Wohlschlegel

    (Seattle)

  • Aric Prieve

    (Seattle)

  • Mervyn G. Thomas

    (The University of Leicester)

  • Thomas A. Reh

    (Seattle)

  • Yumei Li

    (Baylor College of Medicine)

  • Ala Moshiri

    (Sacramento)

  • Rui Chen

    (Baylor College of Medicine
    Baylor College of Medicine
    Baylor College of Medicine
    University of California Irvine School of Medicine)

Abstract

The development of the retina is under tight temporal and spatial control. To gain insights into the molecular basis of this process, we generate a single-nuclei dual-omic atlas of the human developing retina with approximately 220,000 nuclei from 14 human embryos and fetuses aged between 8 and 23-weeks post-conception with matched macular and peripheral tissues. This atlas captures all major cell classes in the retina, along with a large proportion of progenitors and cell-type-specific precursors. Cell trajectory analysis reveals a transition from continuous progression in early progenitors to a hierarchical development during the later stages of cell type specification. Both known and unrecorded candidate transcription factors, along with gene regulatory networks that drive the transitions of various cell fates, are identified. Comparisons between the macular and peripheral retinae indicate a largely consistent yet distinct developmental pattern. This atlas offers unparalleled resolution into the transcriptional and chromatin accessibility landscapes during development, providing an invaluable resource for deeper insights into retinal development and associated diseases.

Suggested Citation

  • Zhen Zuo & Xuesen Cheng & Salma Ferdous & Jianming Shao & Jin Li & Yourong Bao & Jean Li & Jiaxiong Lu & Antonio Jacobo Lopez & Juliette Wohlschlegel & Aric Prieve & Mervyn G. Thomas & Thomas A. Reh &, 2024. "Single cell dual-omic atlas of the human developing retina," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50853-5
    DOI: 10.1038/s41467-024-50853-5
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    References listed on IDEAS

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    2. Michael Lawrence & Wolfgang Huber & Hervé Pagès & Patrick Aboyoun & Marc Carlson & Robert Gentleman & Martin T Morgan & Vincent J Carey, 2013. "Software for Computing and Annotating Genomic Ranges," PLOS Computational Biology, Public Library of Science, vol. 9(8), pages 1-10, August.
    3. Junyue Cao & Malte Spielmann & Xiaojie Qiu & Xingfan Huang & Daniel M. Ibrahim & Andrew J. Hill & Fan Zhang & Stefan Mundlos & Lena Christiansen & Frank J. Steemers & Cole Trapnell & Jay Shendure, 2019. "The single-cell transcriptional landscape of mammalian organogenesis," Nature, Nature, vol. 566(7745), pages 496-502, February.
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