Transposase Spatial Tagging for Genomic DNA Analysis
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Solution Overview
Problem
Conventional methods for studying cellular heterogeneity, such as ATAC-Seq and ChIP-Seq, are limited in their ability to spatially resolve the three-dimensional structures and associated genes that promote cellular variation, failing to provide comprehensive epigenomic insights within the spatial context of a biological sample.
Innovation Solution
The method involves using a transposome to fragment genomic DNA and capture the fragmented DNA on a spatial array with capture probes containing spatial barcodes, allowing for the determination of genomic DNA accessibility and location within a biological sample, enabling spatial analysis of nucleic acids and epigenomic insights.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional ATAC-Seq and ChIP-Seq methods are used to study cellular heterogeneity, then analyte data can be obtained, but spatial resolution and native spatial context information are lost
Solution Approach 1:
The biological sample is divided into discrete spatial locations or regions, with each location assigned a unique spatial barcode. This segmentation allows individual cells or regions to be identified and analyzed separately while maintaining their spatial relationships in the original tissue architecture.
Solution Approach 2:
The patent adds a spatial dimension to conventional sequencing methods by incorporating spatial barcodes that encode location information. This transforms the analysis from purely molecular composition to include spatial positioning, enabling three-dimensional mapping of genomic accessibility within tissue contexts.
2Measurement precision
If spatial array methods are implemented to retain native spatial context, then spatial resolution is improved, but device complexity and method complexity increase
Solution Approach 1:
The spatial array platform is designed to perform multiple functions: it captures spatial location information via barcodes, preserves native tissue architecture, enables genomic DNA accessibility analysis, and maintains cell-cell interaction contexts. This multi-functionality reduces the need for separate specialized devices for each analytical goal.
Solution Approach 2:
Spatial barcodes serve as intermediaries that link physical location in the tissue to digital data in sequencing results. These barcodes act as mediators that encode spatial information without requiring complex imaging or positioning systems, simplifying the overall device architecture.
3Quantity of substance
If transposome-mediated fragmentation is used to analyze accessible chromatin, then epigenomic data is obtained, but spatial location information is lost without spatial barcoding
Solution Approach 1:
The patent merges transposome-mediated chromatin accessibility analysis with spatial barcoding technology. The transposome fragmentation process is combined with the incorporation of spatial barcodes, allowing simultaneous generation of epigenomic data and spatial location information from the same molecular events.
Solution Approach 2:
Spatial barcodes are incorporated into the transposome or associated molecules before the fragmentation and sequencing process. This preliminary tagging ensures that spatial location information is captured at the moment of chromatin accessibility analysis, preventing information loss during subsequent processing steps.
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 provides high spatial resolution analyte and expression data, retaining native spatial context, and enables the identification of genes contributing to cellular function and phenotype by spatially analyzing genomic DNA accessibility.
Implementation Method 1
contacting a transposome to the biological sample to insert transposon end sequences into accessible genomic DNA, thereby generating fragmented genomic DNA
Implementation Method 2
contacting a plurality of splint oligonucleotides to the biological sample, where a splint oligonucleotide hybridizes to the capture domain
Implementation Method 3
ligating the fragmented genomic DNA to the capture probe
Data Source
AI summary
The present disclosure relates to materials and methods for spatially analyzing nucleic acids fragmented with a transposase enzyme in a biological sample.