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. 2017 Oct 13;358(6360):194-199.
doi: 10.1126/science.aan3235. Epub 2017 Aug 31.

The Drosophila Embryo at Single-Cell Transcriptome Resolution

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The Drosophila Embryo at Single-Cell Transcriptome Resolution

Nikos Karaiskos et al. Science. .

Abstract

By the onset of morphogenesis, Drosophila embryos consist of about 6000 cells that express distinct gene combinations. Here, we used single-cell sequencing of precisely staged embryos and devised DistMap, a computational mapping strategy to reconstruct the embryo and to predict spatial gene expression approaching single-cell resolution. We produced a virtual embryo with about 8000 expressed genes per cell. Our interactive Drosophila Virtual Expression eXplorer (DVEX) database generates three-dimensional virtual in situ hybridizations and computes gene expression gradients. We used DVEX to uncover patterned expression of transcription factors and long noncoding RNAs, as well as signaling pathway components. Spatial regulation of Hippo signaling during early embryogenesis suggests a mechanism for establishing asynchronous cell proliferation. Our approach is suitable to generate transcriptomic blueprints for other complex tissues.

Comment in

  • Development: Transcriptomic blueprints.
    Koch L. Koch L. Nat Rev Genet. 2017 Nov;18(11):639. doi: 10.1038/nrg.2017.77. Epub 2017 Sep 18. Nat Rev Genet. 2017. PMID: 28919637 No abstract available.
  • Atlas…t, patterns from every cell.
    Stadler MR, Eisen MB. Stadler MR, et al. Science. 2017 Oct 13;358(6360):172-173. doi: 10.1126/science.aap8493. Science. 2017. PMID: 29026033 No abstract available.

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