Microfluidic Cell Barcoding with Known Barcode Sequences
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Solution Overview
Problem
Current high-throughput cell barcoding methods using beads or gel particles with unknown barcode sequences limit the ability to directly couple a particular transcriptome pattern with a specific individual cell, hindering applications such as precision drug screening and phenotype correlation.
Innovation Solution
A microfluidic approach using valve-based technology for combinatorial assembly of barcoded primers, allowing cells to be labeled with barcodes of known identity, enabling precise correlation of transcriptomes with cell phenotypes by passing cells through a series of valve-operated oligonucleotide inlets to generate microfluidic droplets with known barcodes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If beads or gel particles with combinatorial split-and-pool synthesis are used for barcoding, then high-throughput barcoding is achieved, but the exact barcode sequence becomes unknown and cannot be directly coupled with specific cells
Solution Approach 1:
The barcode synthesis process is segmented into separate sequential steps rather than simultaneous combinatorial synthesis. Each nucleotide position is added in a separate step through valve-controlled inlets, allowing the exact sequence to be determined and recorded while still achieving high-throughput processing of multiple cells
Solution Approach 2:
The system incorporates feedback by recording the exact barcode sequence generated at each step and correlating it with the specific cell it was attached to. This feedback loop ensures that the barcode identity is preserved and can be traced back to the original cell, resolving the information loss problem
2Measurement precision
If valve-operated oligonucleotide inlets are used to feed known barcodes, then direct coupling of transcriptome with cell phenotype is enabled, but device complexity increases
Solution Approach 1:
The microfluidic device uses a universal valve-controlled inlet system that can handle multiple oligonucleotide sequences through the same physical infrastructure. The valves and channels serve multiple functions by sequentially different barcode sequences to different cells, reducing the need for separate dedicated pathways for each barcode
Solution Approach 2:
The system employs a nested structure where multiple oligonucleotide inlets are integrated within a single microfluidic channel system. The valve-controlled inlets are nested within the main flow path, allowing complex barcode assembly through a unified device architecture rather than separate independent systems
Data Source
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AI summary
The present invention relates to the field of microfluidics and in particular to methods for co-localizing a particle comprising DNA and/or RNA with a known barcode oligonucleotide. Thereby, the transcriptome or DNA of a cell can be barcoded and correlated to a cell phenotype or examined for the effect of a drug on the cell. The invention also provides microfluidic devices and systems having properties which make them particularly suitable for use in the methods of the invention.