3D Drosophila embryo model constructed from Stereo-seq dataset

The Drosophila embryo dataset profiled by Stereo-seq [WHL+22] is available at the Flysta3D database (https://db.cngb.org/stomics/flysta3d/). The Drosophila embryo sci-RNA-seq3 dataset [CBGH+22] is available at the GEO DataSets database with accession number GSE190149.

• Reconstrction of 3D Drosophila embryo model using STitch3D
• Applying MCube to the 3D Drosophila embryo model
  • Central nervous system
    • Correcting for slice-specific platform effects
    • Not considering slice-specific platform effects
  • Salivary gland
    • Correcting for slice-specific platform effects
    • Not considering slice-specific platform effects

References

[CBGH+22]

Diego Calderon, Ronnie Blecher-Gonen, Xingfan Huang, Stefano Secchia, James Kentro, Riza M Daza, Beth Martin, Alessandro Dulja, Christoph Schaub, Cole Trapnell, and others. The continuum of \textit Drosophila embryonic development at single-cell resolution. Science, 377(6606):eabn5800, 2022.

[WHL+22]

Mingyue Wang, Qinan Hu, Tianhang Lv, Yuhang Wang, Qing Lan, Rong Xiang, Zhencheng Tu, Yanrong Wei, Kai Han, Chang Shi, and others. High-resolution 3D spatiotemporal transcriptomic maps of developing \textit Drosophila embryos and larvae. Developmental Cell, 57(10):1271–1283, 2022.