Three-dimension transcriptomics maps of whole mouse embryo during organogenesis
Cheng, M.; Zheng, H.; Fang, Q.; Bai, Y.; Liu, C.; Pan, H.; Zhang, Z.; Lu, Q.; Shi, C.; Xia, T.; Jing, Z.; Liu, H.; Feng, N.; Fu, G.; Li, Y.; Feng, J.; Li, Z.; Wang, J.; Chen, Y.; Wang, L.; Deng, Z.; Li, M.; Liu, L.; Chen, A.; Xu, X.
Show abstract
Understanding mammalian development heavily relies on classical animal models like the house mouse (Mus musculus). Advanced spatial transcriptomics has enabled biologists to break new ground in studies of molecular dynamics and cellular patterning during embryonic development with spatiotemporal resolution. To construct a comprehensive developmental trajectory, current three-dimensional (3D) spatial transcriptomic profiling leverages mouse embryos from gastrulation (E5.5) to organogenesis (E13.5) in continuity. However, a crucial phase for early organogenesis between E9.5 and E11.5 was deficient. To unveil the mystery of this stage, we present the 3D transcriptomics of mouse embryos at E9.5 and E11.5, with a widely applicable reconstruction workflow that bypasses sophisticated bioinformatic calculations. As our 3D atlas is generated at single-cell resolution, we demonstrate how organogenetic processes can be interpreted at different levels of granularity, from local cellular interactions to whole embryonic regionalization. We release the open-access database MOSTA3D (Mouse Organogenesis Spatiotemporal Transcriptomic Atlas in Three-dimensional) and hope a broader community will contribute to extending this framework from conception to senility in the near future.
Matching journals
The top 6 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Tbx1 stabilizes differentiation of the cardiopharyngeal mesoderm and drives morphogenesis in the pharyngeal apparatus 96%
- Acto3D: user- and budget-friendly software for multichannel high-resolution three-dimensional imaging 95%
- A single-cell transcriptomic atlas of sensory-dependent gene expression in developing mouse visual cortex 94%
Similar papers in this journal
- Expression of a Barhl1a reporter in subsets of retinal ganglion cells and commissural neurons of the developing zebrafish brain 94%
- Enhanced FGFR3 activity in post-mitotic principal neurons during brain development results in cortical dysplasia and axon miswiring 94%
- Topological data analysis of pattern formation of human induced pluripotent stem cell colonies 94%
Similar papers in this journal
- Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples 96%
- Uncovering Transcriptional Dark Matter via Gene Annotation Independent Single-Cell RNA Sequencing Analysis 96%
- Stripenn detects architectural stripes from chromatin conformation data using computer vision 95%
Similar papers in this journal
- Integrative Analysis of Spatial Transcriptome with Single-cell Transcriptome and Single-cell Epigenome in Mouse Lungs after Immunization 95%
- A spatially-tracked single cell transcriptomics map of neuronal networks in the intrinsic cardiac nervous system 95%
- Comprehensive single-cell atlas of the mouse retina 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.