Projects per year
Abstract / Description of output
Biofoundries are automated high-throughput facilities specializing in the design, construction, and testing of engineered/synthetic DNA constructs (plasmids), often from genetic parts. A critical step of this process is assessing the fidelity of the assembled DNA construct to the desired design. Current methods utilized for this purpose are restriction digest or PCR followed by fragment analysis and sequencing. The Edinburgh Genome Foundry (EGF) has recently established a single-molecule sequencing quality control step using the Oxford Nanopore sequencing technology, along with a companion Nextflow pipeline and a Python package, to perform in-depth analysis and generate a detailed report. Our software enables researchers working with plasmids, including biofoundry scientists, to rapidly analyze and interpret sequencing data. In conclusion, we have created a laboratory and software protocol that validates assembled, cloned, or edited plasmids, using Nanopore long-reads, which can serve as a useful resource for the genetics, synthetic biology, and sequencing communities.
Original language | English |
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Pages (from-to) | 683-686 |
Number of pages | 4 |
Journal | ACS Synthetic Biology |
Volume | 13 |
Issue number | 2 |
Early online date | 8 Feb 2024 |
DOIs | |
Publication status | Published - 16 Feb 2024 |
Keywords / Materials (for Non-textual outputs)
- biofoundry
- DNA assembly
- plasmid validation
- sequencing
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GREET: Generative Recombinant Enzyme Engineering for Therapeutics
Stracquadanio, G. & Rosser, S.
1/01/22 → 31/12/25
Project: Research
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SynthSys-Mammalian: Edinburgh Mammalian Synthetic Biology Research Centre
Rosser, S., Bird, A., Cai, Y., Earnshaw, B., Millar, A., Molina, N., Pilizota, T., Swain, P. & Waites, W.
14/11/14 → 31/03/22
Project: Research