Dual-Substrate Spatial Transcriptomics Capture System
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Solution Overview
Problem
Current spatial transcriptomics methods using multiple substrates suffer from resolution losses due to random diffusion of analytes, which limits the accuracy of detecting the position and abundance of analytes in biological samples.
Innovation Solution
The method involves using two substrates with capture probes, where one substrate has a poly-thymine sequence and the other has spatial barcodes, allowing analytes to passively diffuse and be captured on both, thereby reducing diffusion and increasing spatial resolution by capturing analytes closer to their origin.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If analytes are allowed to diffuse freely in multiple substrate methods, then analyte capture coverage is improved, but spatial resolution deteriorates due to random diffusion
Solution Approach 1:
The patent applies preliminary action by placing capture probes directly on the biological sample before permeabilization. This allows transcripts near the tissue slide surface to be captured in situ before they can diffuse away, thereby reducing spatial broadening while still enabling comprehensive analyte capture through the subsequent permeabilization step
Solution Approach 2:
The patent introduces a third dimension by using a sandwich configuration with substrates on both sides of the biological sample. The first substrate captures analytes from one side while the second substrate captures analytes from the opposite side, effectively dividing the diffusion space and reducing lateral diffusion distance, thereby improving spatial resolution without compromising capture coverage
2Device complexity
If capture probes are placed only on one substrate, then device complexity is reduced, but spatial resolution deteriorates due to increased diffusion distance
Solution Approach 1:
The patent segments the capture function across two substrates, with each substrate bearing capture probes. This segmentation divides the diffusion space into two zones, reducing the maximum diffusion distance for analytes and thereby improving spatial resolution. The segmentation approach maintains relative simplicity while achieving enhanced resolution
Solution Approach 2:
The patent transitions from a single-substrate two-dimensional capture surface to a dual-substrate three-dimensional sandwich configuration. This dimensional change allows capture probes to be positioned on both sides of the biological sample, effectively reducing diffusion distance and improving spatial resolution without excessive complexity
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This approach enhances the spatial resolution of analyte detection, allowing for more accurate determination of analyte abundance and location within biological samples by reducing lateral diffusion and maintaining native spatial context.
Implementation Method 1
The probes on the first slide are arranged on a lawn across the slide and include a capture domain sequence such as a poly d(T) (e.g., an oligo d(T)) sequence
Implementation Method 2
Multiple substrate methods utilize random diffusion of the analyte, thus decreasing the resolution on the barcoded substrate
Implementation Method 3
The second slide which also includes an array of capture probes, and the probes on the second slide include at least a capture domain sequence and spatial barcode
Data Source
AI summary
Provided herein are methods of enhancing spatial resolution of an analyte using sandwich maker system. The methods and systems used herein include a first substrate that includes a plurality of probes that include poly-thymine sequence and a second substrate that includes a plurality of probes comprising a capture domain and a spatial domain.