Single-Cell Sample Indexing for Joint Protein and Gene Readout
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current technologies are limited in their ability to simultaneously quantify protein expression and gene expression in single cells and determine protein-protein interactions, necessitating improved systems and methods for comprehensive analysis.
Innovation Solution
A method involving sample indexing compositions with antigen binding reagents and oligonucleotides, followed by barcoding and sequencing, allows for the identification of sample origins and interactions by attaching cell-specific barcodes to poly(A) mRNA molecules, enabling simultaneous measurement of gene and protein expression.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If current technology is used for measuring gene expression in single cells, then measurement of gene expression can be achieved in a massively parallel manner, but the ability to simultaneously quantify protein expression and determine protein-protein interactions is limited
Solution Approach 1:
The single-cell analysis system is designed to perform multiple functions simultaneously: measuring gene expression via mRNA sequencing, quantifying protein expression through antibody-bound oligonucleotide detection, and determining protein-protein interactions via proximity-based barcoding. This multi-functional approach allows one system to replace multiple separate assays, achieving both high throughput and comprehensive measurement capability.
Solution Approach 2:
The patent combines previously separate measurement techniques into a unified workflow: gene expression analysis and protein expression analysis are merged into a single parallel processing system where cells are barcoded and analyzed together through integrated sequencing workflows, enabling simultaneous quantification of both mRNA and protein levels from the same cell population.
2Measurement precision
If sample indexing compositions with multiple antigen binding reagents are used, then identification of sample origins and protein-protein interactions can be achieved, but the complexity of the system increases
Solution Approach 1:
The system segments the complex measurement task into distinct functional modules: (1) sample indexing compositions with specific antigen binding reagents for different samples, (2) barcoding reagents for cell identification, (3) proximity detection mechanisms for interaction analysis, and (4) sequencing workflows for data generation. Each module performs a specific function, making the overall complex system manageable and scalable.
Solution Approach 2:
Oligonucleotide barcodes serve as intermediary molecules that bridge multiple measurement functions. These barcodes are attached to antibodies bound to proteins, and also contain sample indexing sequences that identify the origin sample. This intermediary approach allows the system to simultaneously track protein identity, sample origin, and interaction partners without requiring direct complex interactions between all components.
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 quantitative analysis of protein expression and protein-protein interactions in cells, facilitating the identification of sample origins through sequencing data analysis.
Implementation Method 1
at least one of the two or more antigen binding reagents is capable of specifically binding to at least one of the one or more antigen targets
Implementation Method 2
the sample indexing oligonucleotide comprises a sample indexing sequence
Data Source
AI summary
Disclosed herein include systems, methods, compositions, and kits for sample identification. A sample indexing composition can comprise, for example, a protein binding reagent associated with a sample indexing oligonucleotide. Different sample indexing compositions can include sample indexing oligonucleotides with different sequences. Sample origin of cells can be identified based on the sequences of the sample indexing oligonucleotides. Sample indexing oligonucleotides can be barcoded using barcoded and lengthened using daisy-chaining primers.