Universal Transposome for Single-Cell Sequencing
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Solution Overview
Problem
Current single-cell genomic techniques require custom modified transposons for labeling nucleic acids, which is costly and challenging for comprehensive sequencing of rare cells without enrichment.
Innovation Solution
A method using a transposome complex with a universal sequence that does not require custom modified transposons, allowing for the incorporation of index sequences into DNA nucleic acids, enabling the generation of sequencing libraries from single nuclei or cells without the need for custom transposon production.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If custom modified transposons are used for single-cell combinatorial indexing, then unique labeling of nucleic acids is achieved, but the cost and complexity of producing custom transposons increases significantly
Solution Approach 1:
The patent uses a standardized transposon sequence that can be repeatedly copied and used across multiple transposome complexes, eliminating the need to produce custom modified transposons for each experiment. The standardized sequence serves as a template that can be replicated indefinitely without modification.
Solution Approach 2:
The standardized transposon sequence is designed to be universally applicable across different single-cell combinatorial indexing experiments. Instead of creating specialized transposons for each application, the same standardized sequence performs the unique labeling function in all cases, making the system multi-functional and broadly applicable.
2Manufacturing precision
If comprehensive sequencing of rare cells is performed without enrichment, then complete characterization of cell populations is achieved, but the cost increases due to custom transposon requirements
Solution Approach 1:
The patent employs a standardized transposon sequence that can be synthesized inexpensively and used in large quantities. Instead of investing in expensive custom transposon production, the approach uses affordable, standardized sequences that can be discarded after use, making comprehensive sequencing of rare cells economically feasible.
Solution Approach 2:
The patent changes the key parameter from custom-modified transposons to standardized transposon sequences. This parameter change fundamentally alters the cost structure, allowing comprehensive sequencing of rare cells without the prohibitive expenses associated with custom transposon synthesis and modification.
3Ease of manufacture
If transposome complex is used without custom modified transposons, then the process simplification is achieved, but the indexing capability must be maintained
Solution Approach 1:
The standardized transposon sequence is designed to inherently provide the indexing capability through its structure. The sequence contains built-in features that enable unique labeling without requiring additional custom modifications, allowing the transposome complex to perform both insertion and indexing functions using the same standardized component.
Solution Approach 2:
The standardized transposon sequence is divided into functional segments that provide different capabilities. These segments include regions for unique labeling, adapter binding, and other necessary functions, allowing the sequence to maintain full indexing capability while using a standardized, non-custom design.
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 approach simplifies the process of creating sequencing libraries and allows for the characterization of rare cells by enabling comprehensive sequencing without the need for costly custom transposon production, facilitating the identification and characterization of subpopulations of cells.
Implementation Method 1
contacting the plurality of nuclei or cells with a transposome complex that includes a transposase and a universal sequence... conditions suitable for incorporation of the universal sequence into DNA nucleic acids
Data Source
AI summary
Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the sequencing library includes nucleic acids that represent the chromatin accessibility from the plurality of single cells. In one embodiment, the nucleic acids include three index sequences. In another embodiment, the present disclosure provides methods for characterizing rare events in isolated cells and nuclei.