Spatially Tagged Genomic DNA Analysis Using Transposase Barcodes
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Solution Overview
Problem
Existing methods for studying spatial heterogeneity in biological samples fail to provide comprehensive data on the position of single cells within tissues and do not account for differences in chromatin structure between cells, limiting the understanding of gene expression and cellular function.
Innovation Solution
A method involving transposase-mediated spatial tagging of genomic DNA using capture probes with spatial barcodes, allowing for the spatial analysis of fragmented genomic DNA by correlating probe locations with sample positions, thereby enabling detailed spatial analysis of genomic DNA and RNA.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of information
If existing methods for studying spatial heterogeneity are used, then some data on analytes can be obtained, but comprehensive spatial information including cell position and chromatin structure differences is lost
Solution Approach 1:
The method embeds multiple layers of information within the DNA fragments themselves: spatial barcodes that encode position information, chromatin accessibility data from ATAC-seq, and gene expression data from RNA-seq. These nested information layers are all contained within the same fragmented DNA molecules, allowing comprehensive spatial and molecular information to be retained and analyzed together without requiring separate complex measurement systems
Solution Approach 2:
The transposase-mediated tagmentation process serves multiple functions simultaneously: it fragments the genomic DNA, adds spatial barcodes to the fragments, and preserves chromatin accessibility information. This multi-functional approach eliminates the need for separate procedures to obtain spatial, epigenetic, and transcriptional data, thereby reducing overall method complexity while preventing information loss
2Quantity of substance
If single-cell analyte data is provided, then detailed gene expression information is obtained, but spatial position information is lost
Solution Approach 1:
The method performs preliminary spatial tagging of genomic DNA fragments with unique spatial barcodes before any cell dissociation or single-cell processing occurs. This preliminary action ensures that position information is permanently encoded in the DNA fragments themselves, so even when DNA is extracted and processed at single-cell resolution, the original spatial context is preserved and can be correlated with gene expression data
3Ease of operation
If tissue permeabilization is performed, then genomic DNA becomes accessible for analysis, but chromatin structure differences may be altered
Solution Approach 1:
The transposase-mediated tagmentation is performed continuously on the permeabilized tissue sections without complete DNA extraction or cell dissociation. The transposase enzyme acts in situ on the accessible chromatin regions, maintaining the continuous connection between chromatin structure and spatial position throughout the process. This continuous action allows DNA accessibility and chromatin structure information to be captured simultaneously without disruption
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
Enables comprehensive spatial analysis of genomic DNA and RNA within biological samples, retaining native spatial context and providing insights into gene expression and cellular function at high resolution.
Implementation Method 1
providing a transposon sequence and a transposase enzyme to the biological sample under conditions wherein the transposon sequence is inserted into the genomic DNA
Implementation Method 2
allowing the transposase enzyme to excise the inserted transposon sequence from the genomic DNA thus generating fragmented genomic DNA
Implementation Method 3
contacting the biological sample comprising the fragmented genomic DNA with an array under conditions such that a capture probe interacts with the fragmented genomic DNA
Data Source
AI summary
The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.