Universal Cell Barcoding via Surface Biotinylation
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Solution Overview
Problem
Current single-cell RNA-seq analysis methods face challenges in accurately capturing gene expression changes in heterogeneous cell populations and are costly and labor-intensive, especially when analyzing multiple samples over time, with batch effects complicating data interpretation and limiting the applicability to all cell types due to reliance on specific cell surface antigens.
Innovation Solution
A universal surface biotinylation method that directly or indirectly brings cell surface proteins into contact with modified barcodes, allowing for biotinylation of any cell surface protein and subsequent labeling with barcoded biotin binding substances, enabling comprehensive labeling of all cell types without dependence on specific antigens.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If antibody-based cell hashing method is used for multiplexing, then cell labeling can be achieved, but it cannot label cells that do not express specific surface antigens such as CD45 or MHC Class I
Solution Approach 1:
The invention uses biotinylated antibodies that can bind to pan-human or pan-mouse surface antigens, making the labeling method universally applicable to all human or mouse cells regardless of their specific cell type or differentiation state, thereby resolving the limitation of antibody-based methods that fail to label cells lacking specific surface antigens
2Measurement precision
If scRNA-seq analysis is performed on multiple samples separately, then each sample can be analyzed individually, but batch effects occur and analysis cost increases
Solution Approach 1:
The invention combines multiple samples into a single scRNA-seq library by labeling cells from different samples with unique barcodes and mixing them before library preparation, allowing simultaneous analysis of multiple samples in one experiment, which reduces batch effects and lowers per-sample analysis costs while maintaining data accuracy
3Productivity
If droplet scRNA-seq or microwell-based scRNA-seq is used, then high-throughput analysis is achieved, but multiple cell contamination errors occur
Solution Approach 1:
The invention introduces barcoded antibodies as an intermediary layer between cells and the scRNA-seq library preparation process. Each cell is labeled with a unique barcode via antibody binding, allowing precise tracking and identification of single-cell origins even in high-throughput droplet or microwell systems, thereby reducing multiple cell contamination errors while maintaining high throughput
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 method provides a versatile, cost-effective, and efficient means for multiplexed single-cell RNA-seq analysis, capable of labeling both viable and fixed cells, including those previously inaccessible, such as pluripotent stem cells and chondrocytes, while minimizing batch effects and maintaining cell viability and differentiation potential.
Implementation Method 1
a first modified barcode that directly or indirectly binds to a cell surface protein of the cell
Implementation Method 2
biotinylating cell surface proteins of the cell... bringing each cell group or each single cell into contact with a barcoded biotin binding substance
Data Source
Figure 1~2
Figure 3
Figure 4A~4C
AI summary
The present invention relates to a method for labeling a cell with a barcode. The method for labeling a cell with a barcode of the invention includes (1) for a cell group containing a plurality of single cells, directly or indirectly bringing a cell surface protein of the cell into contact with a modified barcode; or (2) directly or indirectly bringing a cell surface protein of a single cell into contact with a modified barcode.