High-Density Spatial Barcoding for Single-Cell Location Mapping
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Solution Overview
Problem
Existing spatial analysis techniques fail to provide information on the position of single cells within a biological sample, limiting the understanding of spatial heterogeneity and analyte distribution.
Innovation Solution
Methods involving high-density spatial barcoding using capture probes with spatial barcodes and capture domains to determine the location and abundance of analytes like DNA, RNA, or proteins within a biological sample, including hybridization, ligation, and sequencing of probe oligonucleotides to generate spatially barcoded nucleic acids.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If multiple spatial barcodes are used to identify analyte locations, then measurement precision and spatial resolution are improved, but device complexity and protocol complexity increase
Solution Approach 1:
The spatial barcoding system is segmented into multiple independent barcode components (e.g., first spatial barcode, second spatial barcode) that can be individually synthesized, validated, and applied. Each barcode segment corresponds to specific spatial coordinates, allowing the complex spatial identification task to be divided into manageable modular units that reduce overall system complexity while maintaining high resolution
Solution Approach 2:
The patent transitions from single-dimension barcoding to multi-dimensional spatial barcoding by implementing multiple barcode layers or types (e.g., different barcode chemistries, orientations, or hierarchical levels). This dimensional expansion enables precise 2D or 3D spatial mapping of analytes while the modular nature of each dimension keeps the implementation complexity manageable through systematic design
2Loss of information
If high-density spatial barcoding is implemented, then information completeness about spatial heterogeneity is improved, but loss of time in processing and analysis increases
Solution Approach 1:
Spatial barcodes are pre-synthesized, pre-validated, and pre-mapped to specific spatial coordinates before the actual spatial analysis experiment. Reference libraries of spatial barcode sequences and their corresponding locations are prepared in advance, allowing rapid matching and identification during data analysis without time-consuming computational deconvolution, thus reducing processing time while maintaining complete spatial information
Solution Approach 2:
The patent uses nucleic acid-based spatial barcodes that can be amplified and sequenced using high-throughput copying techniques. Multiple copies of barcoded analytes are generated through PCR or other amplification methods, enabling parallel processing of numerous spatial locations simultaneously. This copying approach maintains complete spatial information while dramatically reducing analysis time through parallelization
3Ease of operation
If capture probes are released from substrate for downstream processing, then ease of operation is improved, but loss of substance increases due to potential loss during release
Solution Approach 1:
A reversible linker or intermediary molecule connects the capture probe to the substrate, allowing controlled release through specific chemical or biological triggers (e.g., pH change, enzymatic cleavage, light exposure). This intermediary mechanism enables clean detachment of capture probes from the substrate with minimal degradation or loss, facilitating downstream processing while preserving probe integrity and reducing substance loss
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
Enhances the understanding of spatial heterogeneity by accurately determining the location and abundance of analytes, facilitating downstream processing and analysis of biological samples.
Implementation Method 1
hybridizing a first probe oligonucleotide and a second probe oligonucleotide to the target nucleic acid
Implementation Method 2
coupling the first probe oligonucleotide and the second probe oligonucleotide, thereby generating a ligation product
Data Source
AI summary
The present disclosure features methods, compositions, and kits for multiple barcoding, high-density barcoding, and/or selective release of barcoded capture probes to capture analytes, or proxies thereof, from a biological sample.