Fluorescent Oligonucleotide Marker Components for Cell Tracking
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Solution Overview
Problem
Current methods fail to efficiently track and analyze large numbers of embedded biological samples in 3D cell culture, particularly rare cells, due to the inability to uniquely identify and assign analysis data to individual entities, which is complicated by non-optical destructive analyses.
Innovation Solution
A marker system comprising a support structure with unique oligonucleotide sequences and fluorophores allows for optical and sequencing-based identification of discrete entities, enabling the assignment of imaging and sequencing data through complementary oligonucleotide hybridization and fluorescent properties.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If large numbers of cells are analyzed to identify rare cells, then the probability of finding rare cells increases, but the complexity of tracking and managing individual entities increases
Solution Approach 1:
The system divides the population of cells into individually trackable units by embedding each cell in a separate hydrogel bead. This segmentation allows high-throughput analysis (millions of cells) while maintaining the ability to track and identify individual entities through unique markers on each bead.
Solution Approach 2:
Unique DNA barcodes and fluorescent markers serve as intermediaries between the physical cell entities and the data tracking system. These markers enable automated identification and correlation of imaging data with sequencing data without requiring direct manual tracking of each cell.
2Adaptability or versatility
If multiple types of analyses are performed on embedded cells, then comprehensive data can be obtained, but the ability to maintain optical tracking becomes compromised due to destructive analyses
Solution Approach 1:
The system creates a genetic copy (DNA barcode sequence) of the identification information that is independent of the optical markers. This allows the optical markers to be used for imaging while the DNA sequences serve as permanent records that can be retrieved and analyzed separately, even after the cell is destroyed by sequencing or other analyses.
Solution Approach 2:
The system combines multiple identification methods (optical markers and DNA barcodes) into a single integrated approach. This merging provides redundancy and allows the system to maintain identification capability through multiple channels, ensuring that loss of one method does not compromise overall tracking ability.
3Measurement precision
If unique identification markers are assigned to each discrete entity, then individual tracking is enabled, but the complexity of the marker system increases
Solution Approach 1:
The DNA barcode markers serve multiple functions: they provide unique identification, enable sequencing-based tracking, and can be correlated with imaging data. This multi-functionality reduces the need for separate specialized markers for each purpose, simplifying the overall system while maintaining high precision identification.
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 efficient tracking and analysis of individual embedded biological samples by correlating imaging and sequencing data, facilitating precise identification and isolation of rare cells in 3D cell culture.
Implementation Method 1
at least a second oligonucleotide at least partially complementary to a part of the first oligonucleotide
Implementation Method 2
at least one label directly or indirectly connected to the second oligonucleotide
Data Source
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AI summary
A constituent part (100, 204, 300, 302, 402, 404, 500) of a marker is provided for marking or for identifying discrete entities (200, 400) comprising: a support structure (102, 304); at least one first oligonucleotide (104, 306) connected to the support structure (102, 304); at least a second oligonucleotide (106) at least partially complementary to a part (108, 310) of the first oligonucleotide (104, 306); and at least one label (112) directly or indirectly connected to the second oligonucleotide (106). In another aspect, a method is provided for assigning sequencing data to imaging data of biological samples (202).