Nucleic Acid Array Spatial Labeling for Transcriptome Sequencing
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Solution Overview
Problem
Current methods for analyzing the genome or transcriptome of cells are laborious, expensive, and lack precision, especially when trying to detect spatial information at the single-cell or sub-cellular level.
Innovation Solution
A method for generating a population of labeled nucleic acid molecules by using a nucleic acid array with oligonucleotide probes, where each probe has a unique tag sequence, and performing reverse transcription and extension reactions to label the nucleic acid molecules, allowing for high-throughput sequencing and spatial information detection.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional methods are used to collect small tissue regions or single cells for genome or transcriptome analysis, then spatial information can be obtained, but the process is laborious, expensive, and has low precision
Solution Approach 1:
The biological sample is segmented into multiple discrete regions or spots on a solid support surface, with each spot containing oligonucleotide probes that can independently capture and label nucleic acid molecules from specific spatial locations. This segmentation enables parallel processing of multiple spatial regions simultaneously, increasing throughput while maintaining single-cell or sub-cellular level precision.
Solution Approach 2:
The method creates copies of spatial information by capturing nucleic acid molecules from specific spatial locations and attaching them to oligonucleotide probes with unique tag sequences that encode positional information. These tagged copies can then be amplified and sequenced, allowing high-throughput detection without losing spatial resolution.
2Productivity
If traditional methods are used to collect small tissue regions or single cells for genome or transcriptome analysis, then spatial information can be obtained, but the process is laborious and expensive
Solution Approach 1:
The solid support with oligonucleotide probe arrays serves multiple functions: it captures nucleic acid molecules from specific spatial locations, labels them with position-encoded tags, and enables subsequent high-throughput sequencing. This multi-functional approach replaces multiple separate操作步骤 with a single integrated platform, reducing operational complexity while increasing throughput.
Solution Approach 2:
The method changes the parameter of spatial information encoding by using unique tag sequences on oligonucleotide probes to represent different spatial positions. This parameter transformation converts complex spatial coordinates into simple, readable nucleic acid sequences that can be easily processed by high-throughput sequencing machines, simplifying the overall detection process.
3Productivity
If high-throughput sequencing is performed on collected samples, then productivity is improved, but spatial information precision is lost without proper labeling
Solution Approach 1:
Oligonucleotide probes with unique tag sequences serve as intermediaries between the spatial location of nucleic acid molecules and the sequencing process. These probes capture molecules from specific positions and attach position-encoding tags, acting as mediators that preserve spatial information while enabling high-throughput processing. The tags serve as a bridge that translates spatial coordinates into sequence data.
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 high-throughput detection of spatial biomolecular information at the single-cell or sub-cellular level, improving precision and reducing costs compared to existing methods.
Implementation Method 1
each oligonucleotide probe has a different tag sequence Y, and the tag sequence Y has a nucleotide sequence unique to the position of the kind of oligonucleotide probe on the solid support
Implementation Method 2
using a primer A to perform reverse transcription of the RNA (e.g., mRNA) of the biological sample to generate a cDNA strand
Implementation Method 3
annealing a primer B to the cDNA strand generated in (a), and performing an extension reaction to generate a first extension product
Data Source
AI summary
Provided are a method for performing position labeling of nucleic acid molecules, a method for constructing a nucleic acid molecule library for transcriptome sequencing, and a kit for implementing the method.