Photo-Controlled Spatial Barcoding for High-Throughput Cell Sequencing
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Solution Overview
Problem
Existing high-throughput single-cell sequencing methods fail to preserve spatial arrangement information of cells in their original biological context, leading to an incomplete picture of gene expression in complex multi-cellular systems.
Innovation Solution
A method utilizing photo-controlled adapter sequences, nucleic acid tags, and linkers to label or barcode molecules within cells, enabling high-throughput labeling that maintains spatial organization information.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If high-throughput single-cell sequencing methods are used, then sequencing throughput is improved, but spatial arrangement information is lost
Solution Approach 1:
The tissue section is divided into multiple discrete regions of interest (ROIs), each assigned a unique barcode. This segmentation allows parallel processing of multiple regions while preserving their spatial identities through the barcode system, resolving the contradiction between high throughput and spatial information preservation.
Solution Approach 2:
Instead of physically separating and analyzing cells individually (which preserves space but reduces throughput), the invention creates informational copies through barcodes that represent spatial locations. These barcodes are attached to nucleic acids from multiple regions simultaneously, enabling high-throughput sequencing while maintaining spatial information through the barcode copies.
2Measurement precision
If microdissection methods are used, then spatial resolution is improved, but throughput is reduced
Solution Approach 1:
The invention merges the advantages of microdissection (spatial resolution) with high-throughput sequencing by combining physical sectioning with molecular barcoding. Multiple regions are processed simultaneously in a single sequencing run, unlike sequential microdissection, thus achieving both high spatial resolution and high throughput through the combination of these approaches.
Solution Approach 2:
Barcodes representing different spatial regions are prepared and assigned to specific ROIs before the sequencing process. This preliminary barcoding of tissue sections enables subsequent high-throughput processing without losing spatial information, as the spatial identities are already encoded and preserved throughout the sequencing workflow.
3Quantity of substance
If custom oligonucleotide arrays are used, then gene expression coverage is improved, but device complexity and cost increase
Solution Approach 1:
The barcode sequencing approach uses universal sequencing adapters and primers that can detect any nucleic acid sequence, replacing the need for custom arrays designed for specific genes. This universal system provides comprehensive gene expression coverage across the entire transcriptome without requiring separate custom arrays for different measurements, thus reducing device complexity and manufacturing costs.
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
Provides comprehensive spatial organization information of gene expression in cells, allowing for accurate sequencing and analysis of spatially differential RNA expression.
Implementation Method 1
a first region of interest is exposed to light, thereby exposing a 5′ end domain of the photo-controlled adapter sequence
Data Source
AI summary
Methods of labeling or barcoding molecules within one or more portions of a plurality of cells are provided. Kits and systems for labeling or barcoding molecules within one or more portions of a plurality of cells are also provided. The methods, kits, and systems may utilize photo-controlled adapter sequences, nucleic acids tags, and/or linkers.