Cell Indexing Oligonucleotides for Single-Cell Phenotypic Data Association
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Solution Overview
Problem
Current technologies face challenges in effectively associating single cell sequencing data with phenotypic data and agent exposure, particularly in linking gene expression of single cells with their corresponding phenotypic characteristics and drug responses in a massively parallel manner.
Innovation Solution
The method involves labeling cells with cell indexing oligonucleotides, pooling, and distributing them into partitions, where specific indexing oligonucleotides are used to generate unique cell indexing sequences, allowing for the association of phenotypic and sequencing data by stochastic labeling and imaging.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If single cell sequencing data is measured in a massively parallel manner, then productivity is improved, but the ability to associate data with specific phenotypic characteristics deteriorates
Solution Approach 1:
The patent segments the indexing process into multiple rounds, with each round adding a portion of the unique identifier to the oligonucleotide barcode. This allows massively parallel processing while maintaining the ability to trace each cell's phenotypic data through the combined barcode sequence, resolving the contradiction between throughput and data association capability.
Solution Approach 2:
The patent adds a temporal dimension to the indexing process by performing multiple indexing rounds at different time points. Each round contributes to building the complete cell identifier, enabling massive parallelism in the final measurement while preserving the ability to associate results with specific phenotypic characteristics through the accumulated barcode information.
2Measurement precision
If multiple cellular component-binding reagents are used to label cells, then measurement precision is improved, but device complexity increases
Solution Approach 1:
The patent creates a universal indexing system where the same basic process and reagents can be used across multiple indexing rounds and for different cellular components. The modular design allows the same framework to handle protein labeling, RNA sequencing, and phenotypic measurements, reducing overall system complexity while maintaining high measurement precision through the use of multiple specific reagents.
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 enables the efficient association of phenotypic and sequencing data, facilitating the identification of gene expression profiles and agent responses at a single-cell level, thereby improving the understanding of cellular behavior and drug effects.
Implementation Method 1
the cellular component-binding reagent is capable of specifically binding to the one or more cellular component targets
Implementation Method 2
the cell indexing sequence of the cell indexing oligonucleotide comprises the first cell indexing subsequence and the second cell indexing subsequence
Data Source
AI summary
Disclosed herein include systems, methods, compositions, and kits for associating single cell sequencing data with phenotypic data and/or agent exposure. In some embodiments, cell indexing oligonucleotides comprising cell indexing sequences are associated with cells. In some embodiments, synthetic particles are associated with stochastic labels comprising cell indexing sequences. Sequential hybridizing and imaging of probes annealing to a cell indexing sequence can generate a spatial index. The spatial index can be employed to identify of the partition from which a sequenced nucleic acid target molecule originated.