Metabolism is dynamic during early development in animals. To study this process, we developed a single-embryo metabolomics and transcriptomics method that captures rapid, small-scale changes in metabolism and how they coordinate with gene expression. Our work showcasing this method in Drosophila embryos provides a valuable resource for understanding developmental systems biology.
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References
Pérez-Mojica, J. E., Enders, L., Lau, K. H. & Lempradl, A. Single-embryo RNA sequencing for continuous and sex-specific gene expression analysis on. Drosophila. STAR Protoc. 4, 102535 (2023). This protocol has step-by-step instructions for single embryo collection and RNA-seq library preparation.
Hashimshony, T. et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome Biol. 17, 77 (2016). This paper reports the original single-cell RNA-seq protocol we adapted and used for single-embryo RNA-seq.
Herman, J. S., Sagar & Grün, D. FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data. Nat. Methods 15, 379–386 (2018). This paper reports the tools we used to analyse the single-embryo RNA-seq data generated in our study.
Pérez-Mojica, J. E., Enders, L., Walsh, J., Lau, K. H. & Lempradl, A. Continuous transcriptome analysis reveals novel patterns of early gene expression in Drosophila embryos. Cell Genom. 3, 100265 (2023). This paper reports and validates a strategy to identify embryo sex using gene expression data in Drosophila.
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This is a summary of: Pérez-Mojica, J. E. et al. Resolving early embryonic metabolism in Drosophila through single-embryo metabolomics and transcriptomics. Nat. Metab. https://doi.org/10.1038/s42255-025-01351-5 (2025).
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Investigating metabolic changes in single embryos during early development in Drosophila. Nat Metab (2025). https://doi.org/10.1038/s42255-025-01375-x
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DOI: https://doi.org/10.1038/s42255-025-01375-x
