Spatial Barcode Probe Capture for Single-Cell Location Mapping
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Solution Overview
Problem
Existing techniques fail to provide spatial information on the position of single cells within a biological sample, limiting the understanding of spatial heterogeneity and analyte distribution.
Innovation Solution
Methods and systems for capturing probes and barcodes that utilize RNA-templated ligation (RTL) and a 'sandwich process' to transfer analytes from a first substrate to a second substrate for spatial analysis, involving hybridization, ligation, and alignment with an array containing capture probes with spatial barcodes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of information
If traditional techniques are used to analyze analytes in biological samples, then analyte data can be obtained, but spatial information regarding the position of single cells within the tissue is lost
Solution Approach 1:
The patent introduces spatial barcodes as intermediary elements that bridge the analyte and the detection system. These barcodes are incorporated into probe molecules that hybridize to target analytes, allowing spatial information to be captured without directly modifying the complex tissue structure. The barcode sequence encodes positional information that can be decoded later, serving as a mediator between the physical location in tissue and the digital data output.
Solution Approach 2:
The patent segments the spatial information encoding into discrete barcode sequences that can be assigned to specific tissue locations. By dividing the tissue into addressable units with unique barcode identifiers, the system maintains spatial resolution without requiring a monolithic complex detection system. Each probe carries a segmented piece of spatial information that can be independently tracked and reassembled.
2Measurement precision
If RNA-templated ligation and sandwich process are used to transfer analytes, then spatial location and abundance can be precisely determined, but the process complexity increases
Solution Approach 1:
The patent performs preliminary actions by pre-encoding spatial information into barcode sequences that are incorporated into probe molecules before they contact the tissue sample. The probes are pre-prepared with both the capture sequence and the spatial barcode, so that when they hybridize to analytes and are transferred to the array, the spatial information is already embedded and ready for detection, eliminating the need for complex post-processing localization steps.
Solution Approach 2:
The patent merges multiple functions into the probe molecule: analyte hybridization, spatial encoding, and array attachment. By combining the capture sequence, barcode sequence, and attachment functionality into a single integrated probe structure, the system achieves precise spatial measurement without requiring separate complex systems for each function. The sandwich process itself is merged with the barcode transfer, so analyte capture and spatial information transfer occur simultaneously.
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
Enable precise determination of analyte location and abundance, facilitating downstream processing and enhancing the understanding of spatial heterogeneity in biological samples.
Implementation Method 1
hybridizing a first probe oligonucleotide and a second probe oligonucleotide to the analyte, wherein the first probe oligonucleotide and the second probe oligonucleotide each comprise a sequence that is substantially complementary to adjacent sequences of the analyte
Implementation Method 2
migrating the connected probe from the biological sample to the array
Implementation Method 3
hybridizing the connected probe to the capture domain
Data Source
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AI summary
Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.