Lipid-Modified Oligonucleotides for Single-Cell Multiplexing
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Solution Overview
Problem
Current single-cell RNA sequencing methods face limitations in sample multiplexing capacity, efficiency, and cost due to physical constraints of microfluidics devices, leading to high technical noise and reduced informativeness of transcriptome datasets.
Innovation Solution
The use of lipid-modified oligonucleotides for cell barcoding allows for enhanced sample multiplexing by incorporating sample-specific information, enabling the processing of a greater number of single cells without cell doublets and reducing batch effects, through compositions that include lipid-conjugated DNA oligonucleotides with specific hybridization and primer regions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If droplet microfluidics-based single-cell RNA sequencing is used, then single-cell resolution is achieved, but sample multiplexing capacity is limited to eight due to physical constraints of the device
Solution Approach 1:
The patent transitions from spatial multiplexing (limited by physical channels in microfluidics) to chemical multiplexing using lipid-modified oligonucleotides that can be combined in any ratio, effectively adding a new dimension to sample multiplexing capability
Solution Approach 2:
The lipid-modified oligonucleotide barcodes serve multiple functions: they enable sample identification, allow for arbitrary sample combinations, and can be used across different microfluidics devices without being constrained by device-specific channel configurations
2Productivity
If more samples are processed through current microfluidics methods, then throughput increases, but technical noise increases and batch effects are reduced
Solution Approach 1:
Samples are pre-barcoded with lipid-modified oligonucleotides before being combined and processed together, allowing for clear identification and computational separation of samples even when processed in large batches, thereby preventing batch effects and reducing technical noise
3Measurement precision
If commercial droplet microfluidics-based single-cell RNA sequencing is used, then single-cell analysis is performed, but cost is high and efficiency is low
Solution Approach 1:
The patent changes the key parameter from device-channel-based multiplexing to oligonucleotide-concentration-based multiplexing, allowing for flexible and cost-effective scaling of sample numbers without being constrained by expensive device modifications
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 increases the throughput and informativeness of single-cell RNA sequencing datasets, reduces technical noise, and allows for the efficient removal of cell doublets, thereby improving the accuracy and efficiency of single-cell transcriptome analysis.
Implementation Method 1
a first lipid-conjugated DNA oligonucleotide comprising a first lipid moiety, a first hybridization region, and a first primer region
Data Source
AI summary
Disclosed are compositions comprising a first lipid-conjugated oligonucleotide comprising a first lipid moiety, a first hybridization region, and a first primer region; a second lipid-conjugated oligonucleotide comprising a second hybridization region and a second lipid moiety, wherein the second hybridization region is the reverse complement of the first hybridization region; and a third oligonucleotide comprising a second primer region, a barcode region, and a capture sequence, wherein the second primer region is the reverse complement of the first primer region; compositions comprising a lipid-conjugated DNA oligonucleotide comprising a lipid moiety, a barcode region, and a capture sequence; and composition comprising a first lipid-conjugated DNA oligonucleotide comprising a lipid moiety and a first primer region; and a second DNA oligonucleotide comprising a second primer region, a barcode region, and a capture sequence, wherein the second primer region is the reverse complement of the first primer region. Also disclosed are membranes and cells comprising such compositions and uses of such compositions.