PUBLICATION
A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors
- Authors
- Lange, M., Granados, A., VijayKumar, S., Bragantini, J., Ancheta, S., Kim, Y.J., Santhosh, S., Borja, M., Kobayashi, H., McGeever, E., Solak, A.C., Yang, B., Zhao, X., Liu, Y., Detweiler, A.M., Paul, S., Theodoro, I., Mekonen, H., Charlton, C., Lao, T., Banks, R., Xiao, S., Jacobo, A., Balla, K., Awayan, K., D'Souza, S., Haase, R., Dizeux, A., Pourquie, O., Gómez-Sjöberg, R., Huber, G., Serra, M., Neff, N., Pisco, A.O., Royer, L.A.
- ID
- ZDB-PUB-241027-2
- Date
- 2024
- Source
- Cell 187(23): 6742-6759.e17 (Journal)
- Registered Authors
- Balla, Keir, Royer, Loic
- Keywords
- NMPs, RNA velocity, cell state transition, embryonic pluripotency, in silico fate mapping, light-sheet microscopy, lineage reconstruction, neuro-mesodermal progenitors, scRNA-seq, single-cell RNA sequencing, transcriptomic variability, zebrafish developmental atlas
- MeSH Terms
-
- Gene Expression Regulation, Developmental
- Cell Lineage*
- Single-Cell Analysis
- Embryonic Development
- Cell Differentiation
- Atlases as Topic
- Pluripotent Stem Cells/cytology
- Pluripotent Stem Cells/metabolism
- Embryo, Nonmammalian/cytology
- Embryo, Nonmammalian/metabolism
- Animals
- Mesoderm/cytology
- Zebrafish*/embryology
- PubMed
- 39454574 Full text @ Cell
Citation
Lange, M., Granados, A., VijayKumar, S., Bragantini, J., Ancheta, S., Kim, Y.J., Santhosh, S., Borja, M., Kobayashi, H., McGeever, E., Solak, A.C., Yang, B., Zhao, X., Liu, Y., Detweiler, A.M., Paul, S., Theodoro, I., Mekonen, H., Charlton, C., Lao, T., Banks, R., Xiao, S., Jacobo, A., Balla, K., Awayan, K., D'Souza, S., Haase, R., Dizeux, A., Pourquie, O., Gómez-Sjöberg, R., Huber, G., Serra, M., Neff, N., Pisco, A.O., Royer, L.A. (2024) A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors. Cell. 187(23):6742-6759.e17.
Abstract
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping