High-resolution 3D spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae

The continuum of Drosophila embryonic development at single-cell resolution

“…Our single-cell data thus capture the biological variability in enhancer accessibility along the A-P axis, extending previous observations. We similarly could transfer labels from our sci-RNA-seq clusters to spatial coordinates from a spatial enhanced resolution omics sequencing (Stereo-seq)–based spatial study of Drosophila embryos at 14 to 16 hours and 16 to 18 hours of development ( 28 ). Using the assigned annotations of tissues from the spatial study, we observe a correspondence with our cluster annotations, which again suggests the spatial-relevant variability present in these data (fig.…”

Computational solutions for spatial transcriptomics

“…The HDST and Seq-Scope studies demonstrated that the high-resolution arrays can locate even rare cell types and resolve the gene expression differences at subcellular resolution, which makes for example the nuclear-to-cytoplasmic type of RNA-velocity of analysis feasible for spatial barcode ST methods [9] , [25] . The preprints showcase the capabilities and limitations of Stereo-Seq with tumor leading-edge samples [65] and high-resolution spatial transcriptome atlases produced from regenerating axolotl brains and the developmental stages of the mouse, zebrafish, and fruit fly embryos [7] , [66] , [67] , [68] . Already these detailed transcriptome atlases, after being released into the public domain, could provide a rich resource of transcriptomic data to analyze the developmental process and brain regeneration of multicellular organisms.…”

An integrated microfluidic device for multiplexed imaging of spatial gene expression patterns of Drosophila embryos

“…53 RNA-sequencing on cryo-sectioning embryos or single nucleus RNA-seq has been developed to measure the spatial profiles of mRNA in early embryos. 54–56 As for the protein profiles, IF-based multiplexed protein detection techniques with microfluidics also have the potential to overcome the above challenges. However, only a few microfluidic chips have been tested for Drosophila embryos, 38,42,57–61 e.g.…”

“…53 RNA-sequencing on cryo-sectioning embryos or single nucleus RNA-seq has been developed to measure the spatial profiles of mRNA in early embryos. [54][55][56] As for the protein profiles, IF-based multiplexed protein detection techniques with microfluidics also have the potential to overcome the above challenges. However, only a few microfluidic chips have been tested for Drosophila embryos, 38,42,[57][58][59][60][61] e.g., the Drosophila embryos can be trapped by the microfluidic chip with a vertical orientation for imaging the dorsal-ventral patterning profiles, or with a horizontal orientation for live imaging on the anterior-posterior patterning profiles.…”