Padlock Probe-Based Targeted In Situ Sequencing: Overview of Methods and Applications

Area of Science:

• Molecular Biology
• Genomics
• Biotechnology

Background:

• Understanding spatiotemporal gene expression is crucial for studying health, development, and disease.
• Spatially resolved transcriptomics preserves tissue architecture for gene expression profiling, enabling spatial cell atlases and interaction studies.
• In situ cell typing and analysis of cell-cell interactions are key applications driving the field.

Purpose of the Study:

• This review focuses on padlock probe-based in situ sequencing, a targeted method in spatially resolved transcriptomics.
• It aims to summarize recent advancements in methodology and computational tools for this technique.
• Key applications and future integration possibilities with multiomic platforms are discussed.

Main Methods:

• Padlock probe-based in situ sequencing is highlighted as a targeted spatially resolved transcriptomic approach.
• Methodological and computational tool developments are summarized.
• Compatibility with other techniques and multiomic integration are explored.

Main Results:

• Recent methodological and computational advancements have refined targeted spatially resolved transcriptomics.
• Padlock probe-based in situ sequencing enables detailed spatial gene expression analysis.
• The technique shows promise for integration with other methods for comprehensive multiomic studies.

Conclusions:

• Padlock probe-based in situ sequencing is a powerful targeted method for spatially resolved transcriptomics.
• Continued development of tools and integration strategies will expand its applications in biological research.
• This technique is vital for advancing our understanding of complex biological systems.