Method, system and terminal for three-dimensional construction of single-cell spatial transcriptome

By constructing the three-dimensional spatial distribution of single cells using spatial transcriptomics technology and mathematical models, the problem of lost location information in early embryonic development was solved, a high-precision whole-genome spatiotemporal expression database was realized, and the spatial transcriptome map of the embryo was reconstructed.

CN118824347BActive Publication Date: 2026-07-24CENT FOR EXCELLENCE IN MOLECULAR CELL SCI CHINESE ACAD OF SCI +1
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Patent Information

Application Number
CN202310437409.9
Authority / Receiving Office
CN · China
Patent Type
Patents(China)
Current Assignee / Owner
Filing Date
2023-04-21
Publication Date
2026-07-24
Estimated Expiration
2043-04-21

AI Technical Summary

Technical Problem

Existing spatial transcriptomics technology cannot comprehensively, completely, and with high precision study the spatiotemporal dynamic molecular expression patterns of various germ layer patterns in early embryonic development, nor can it restore embryonic tissue cells or pluripotent stem cells to specific locations in the embryo in vivo, nor can it locate the corresponding parts of the embryo in vivo.

Method used

Location-specific data were captured using spatial transcriptomics technology. Two-dimensional and three-dimensional spatial expression patterns were constructed using corn map and three-dimensional corn map models. By combining single-cell transcriptomics data and multi-dimensional single-cell mapping models, the optimal mapping location of single cells was determined. The three-dimensional spatial distribution of single cells was simulated based on spatial simulation and optimization models.

Benefits of technology

It has achieved high-resolution digital in situ hybridization maps of the entire genome with single-cell precision, established the most comprehensive, complete, and accurate interactive spatiotemporal transcriptome database, and reconstructed spatial transcriptome maps of the ecto, meso, and endoderm layers.

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Abstract

The three-dimensional construction method, system and terminal of the single-cell spatial transcriptome of the application capture the position-specific spatial transcriptome data of the mouse early embryo development primitive gut movement period by using the spatial transcriptome technology, and then the spatial transcriptome atlas of the outer, middle and inner germ layers is three-dimensionally reconstructed by establishing a mathematical model, a full-genome space-time expression database is established, the full-genome high-resolution digital in-situ hybridization atlas of the single-cell precision of the mouse embryo development primitive gut movement period is realized, it is the most comprehensive, complete and highest-precision interactive space-time transcriptome database in the world at present. Moreover, the application has the functions of identifying spatial marker genes and spatial positioning of single cells (or cell groups). Meanwhile, the spatial single-cell algorithm contained in the application simulates the spatial distribution of single cells in different germ layers, and further three-dimensionally reconstructs the spatial transcriptome atlas of the single-cell precision, the work provides comprehensive data and brand-new ideas for understanding the germ layer lineage establishment and the fate regulation mechanism of pluripotent stem cells, and promotes the development of the early embryo development and stem cell regenerative medicine related fields.
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