Spatial transcriptomics chips with sequencing-based microscopy

Introduction

We propose a technology platform for low cost, high resolution spatial transcriptomics surfaces. Spatial transcriptomics is a high cost research methodology for resolving the spatial variation of genes in a tissue by capturing mRNA transcripts on a surface containing molecular address markers.

Current Methods

To produce these surfaces, current methods rely on either:

1. Printing technology with explicit assignment of unique address IDs to spatial locations.
2. Random scattering of molecular IDs that are then sequenced in situ using microscopy.

Both of these fabrication methods are prohibitively expensive and time-consuming, such that spatial transcriptomic technology is still limited to a narrow selection of low throughput research applications.

Proposed Technology

Our proposed technology, the MESH CHIP, represents a radically different approach to producing these surfaces. Rather than print surfaces or build sequence-address maps with in situ microscopy, our technology works by self-assembly and deduction from sequencing data alone.

Advantages of MESH CHIP

This means that no prior information about the identity or location of address markers on the surface is needed prior to mRNA capture and sequencing. Instead, this information is reconstructed computationally using graph theory in a post hoc fashion.

By moving this information roadblock in the fabrication process to the increasingly cheap sequencing and computing stage, we greatly improve the cost performance of this technology.

Conclusion

MESH CHIP technology would represent a qualitatively lower cost product with greater performance than the state of the art, unlocking new use cases like diagnostics and high throughput tissue processing.