Protocol for high-resolution 3D spatial transcriptomics using Open-ST

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Spatial transcriptomics (ST) is crucial for dissecting molecular mechanisms in biological tissues.
• Understanding spatial gene expression patterns is key to advancing research in health and disease.

Purpose of the Study:

• To present an efficient and high-resolution protocol for 2D and 3D spatial transcriptomics.
• To introduce Open-ST, a novel computational workflow for generating molecular maps of tissues.

Main Methods:

• Repurposing Illumina flow cells into spatially barcoded capture areas.
• Preparing spatial transcriptomics libraries from stained cryosections.
• Detailed computational workflow for generating 2D/3D molecular maps aligned with histology.

Main Results:

• Development of the Open-ST protocol for efficient and high-resolution spatial transcriptomics.
• Creation of "virtual tissue blocks" that integrate molecular data with spatial information.
• Demonstration of Open-ST's applicability to diverse tissue types, including clinical samples.

Conclusions:

• Open-ST provides a robust method for high-resolution spatial transcriptomics in various tissue types.
• The protocol facilitates the exploration of molecular pathways within their spatial context.
• This approach enhances the understanding of molecular mechanisms in both health and disease.