A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors
Elucidating organismal developmental processes requires a comprehensive understanding of cellular lineages in the spatial, temporal, and molecular domains. In this study, we introduce Zebrahub, a dynamic atlas of zebrafish embryonic development that integrates single-cell sequencing time course data with lineage reconstructions facilitated by light-sheet microscopy. This atlas offers high-resolution and in-depth molecular insights into zebrafish development, achieved through the sequencing of individual embryos across ten developmental stages, complemented by reconstructions of cellular trajectories. Zebrahub also incorporates an interactive tool to navigate the complex cellular flows and lineages derived from light-sheet microscopy data, enabling in silico fate-mapping experiments. To demonstrate the versatility of our multimodal resource, we utilize Zebrahub to provide fresh insights into the pluripotency of neuro-mesodermal progenitors (NMPs) and the origins of a joint kidney-hemangioblast progenitor population.
Authors
- Sarah Ancheta (ORCID: https://orcid.org/0009-0004-2198-2821)
- Rachel A. Banks (ORCID: https://orcid.org/0000-0003-2028-2925)
- Chris Charlton (ORCID: https://orcid.org/0000-0003-2008-9893)
- Ilan Theodoro (ORCID: https://orcid.org/0000-0003-4019-3380)
- Bin Yang (ORCID: https://orcid.org/0000-0001-5138-4663)
- Angela M. Detweiler (ORCID: https://orcid.org/0000-0001-7026-5467)
- Merlin Lange (ORCID: https://orcid.org/0000-0003-0534-4374)
- Jordão Bragantini (ORCID: https://orcid.org/0000-0001-7652-2735)
- Shruthi VijayKumar (ORCID: https://orcid.org/0000-0001-6679-1261)
- Tiger Lao (ORCID: https://orcid.org/0009-0005-6793-8102)
- Yang Liu (ORCID: https://orcid.org/0000-0002-8168-5421)
- Ahmet Can Solak (ORCID: https://orcid.org/0000-0002-1381-8309)
- Sheryl Paul (ORCID: https://orcid.org/0009-0008-7063-2026)
- Kyle Awayan (ORCID: https://orcid.org/0000-0002-4442-3270)
- Löıc A. Royer (ORCID: https://orcid.org/0000-0002-9991-9724)
- Samuel D’Souza (ORCID: https://orcid.org/0009-0003-2607-3742)
- Xiang Zhao (ORCID: https://orcid.org/0000-0002-3339-4806)
- Robert Haase (ORCID: https://orcid.org/0000-0001-5949-2327)
- Rafael Gómez-Sjöberg (ORCID: https://orcid.org/0000-0001-8017-9669)
- Adrián Jacobo (ORCID: https://orcid.org/0000-0001-9381-6292)
- Aaron McGeever (ORCID: https://orcid.org/0000-0003-1596-207X)
- Michael Borja (ORCID: https://orcid.org/0009-0006-4527-3370)
- Norma Neff (ORCID: https://orcid.org/0000-0001-7141-5420)
- Yang Joon Kim (ORCID: https://orcid.org/0000-0003-1742-5657)
- Honey Mekonen (ORCID: https://orcid.org/0009-0001-7959-1151)
- Sreejith Santhosh (ORCID: https://orcid.org/0000-0001-5278-6277)
- Olivier Pourquié (ORCID: https://orcid.org/0000-0001-5189-1227)
- Keir M. Balla (ORCID: https://orcid.org/0000-0003-2474-7953)
- Alexandre Dizeux (ORCID: https://orcid.org/0000-0002-7394-143X)
- Alejandro A. Granados (ORCID: https://orcid.org/0000-0002-6275-9800)
- Mattia Serra (ORCID: https://orcid.org/0000-0002-6007-5878)
- Sheng Xiao (ORCID: https://orcid.org/0000-0001-8959-2388)
- Greg Huber (ORCID: https://orcid.org/0000-0002-8292-4164)
- Hirofumi Kobayashi (ORCID: https://orcid.org/0000-0002-4505-2061)
Institutions
- Harvard University (US)
- University of California San Diego (US)
- Chan Zuckerberg Initiative (United States) (US)
- Physique pour la médecine Paris (FR)
- Technische Universität Dresden (DE)
- ESPCI Paris (FR)
Publication Details
- Journal
- Cell
- Published
- 2024-10-24
- DOI
- https://doi.org/10.1016/j.cell.2024.09.047
- Citations
- 80
- Primary Topic
- Congenital heart defects research
- Type
- article
- Field-Weighted Citation Impact
- 18.71