Well-ST-seq: Cost-Effective and Near-Cellular Spatial Transcriptomics Using Deterministic Barcoded Bead Arrays

Area of Science:

• Molecular Biology
• Genomics
• Biotechnology

Background:

• Spatial transcriptomics enables detailed tissue analysis but faces challenges in balancing resolution, cost, and sensitivity.
• Deterministic probe array methods require optimization for broader research and clinical use.

Purpose of the Study:

• To introduce Well-ST-seq, a novel platform for cost-efficient, near-cellular resolution spatial transcriptomics.
• To demonstrate the platform's capability for rapid fabrication and high-quality transcript recovery.

Main Methods:

• Integration of microwell-assembled hydrogel bead carriers with combinatorial microfluidic indexing.
• Utilizing orthogonal microchannels for coordinate indexing and simplified probe construction on bead carriers.
• Preparation of spatially barcoded capture arrays within approximately 2 hours.

Main Results:

• Achieved a direct consumables cost of ~$0.05-$0.54 per mm² for 10-30 μm spot sizes.
• Demonstrated high transcript recovery (3,896 UMIs per spot) in mouse hippocampus using 10 μm arrays.
• Enabled delineation of layered organization, region-specific expression, and coherent alignment across serial sections of developing mouse brain.

Conclusions:

• Well-ST-seq offers a rapid and cost-efficient method for fabricating deterministic spatial transcriptomics slides.
• The platform provides near-cellular spatial tissue profiling capabilities, advancing basic research and clinical applications.