A highly parallel strategy for storage of digital information in living cells

Akhmetov, Azat; Ellington, Andrew D.; Marcotte, Edward M.

doi:10.1101/096792

Cited by 5 publications

(6 citation statements)

References 23 publications

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“…There is increasing interest in using DNA as a medium for information storage ( 64 , 65 ). Recently, researchers began experimenting with storing information in plasmids, as they can be rapidly replicated ( 66 , 67 ). A technology for encrypting and securing digital information using cybersecurity techniques has also been developed for plasmids ( 36 , 37 ).…”

Section: Discussionmentioning

confidence: 99%

Rapid, robust plasmid verification by de novo assembly of short sequencing reads

Gallegos

Rogers²,

Cialek

et al. 2020

Nucleic Acids Research

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Plasmids are a foundational tool for basic and applied research across all subfields of biology. Increasingly, researchers in synthetic biology are relying on and developing massive libraries of plasmids as vectors for directed evolution, combinatorial gene circuit tests, and for CRISPR multiplexing. Verification of plasmid sequences following synthesis is a crucial quality control step that creates a bottleneck in plasmid fabrication workflows. Crucially, researchers often elect to forego the cumbersome verification step, potentially leading to reproducibility and—depending on the application—security issues. In order to facilitate plasmid verification to improve the quality and reproducibility of life science research, we developed a fast, simple, and open source pipeline for assembly and verification of plasmid sequences from Illumina reads. We demonstrate that our pipeline, which relies on de novo assembly, can also be used to detect contaminating sequences in plasmid samples. In addition to presenting our pipeline, we discuss the role for verification and quality control in the increasingly complex life science workflows ushered in by synthetic biology.

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Section: Discussionmentioning

confidence: 99%

Rapid, robust plasmid verification by de novo assembly of short sequencing reads

Gallegos

Rogers²,

Cialek

et al. 2020

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…There is increasing interest in using DNA as a medium for information storage (58,59). Recently, researchers began experimenting with storing information in plasmids, as they can be rapidly replicated (60,61). A technology for encrypting and securing digital information using cybersecurity techniques has also been developed for plasmids (62).…”

Section: Discussionmentioning

confidence: 99%

Rapid, robust plasmid verification byde novoassembly of short sequencing reads

Gallegos

Rogers²,

Cialek

et al. 2020

Preprint

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AbstractPlasmids are a foundational tool for basic and applied research across all subfields of biology. Increasingly, researchers in synthetic biology are relying on and developing massive libraries of plasmids as vectors for directed evolution, combinatorial gene circuit tests, and for CRISPR multiplexing. Verification of plasmid sequences following synthesis is a crucial quality control step that creates a bottleneck in plasmid fabrication workflows. Crucially, researchers often elect to forego the cumbersome verification step, potentially leading to reproducibility and— depending on the application—security issues. In order to facilitate plasmid verification to improve the quality and reproducibility of life science research, we developed a fast, simple, and open source pipeline for assembly and verification of plasmid sequences from Illumina reads. We demonstrate that our pipeline, which relies on de novo assembly, can also be used to detect contaminating sequences in plasmid samples. In addition to presenting our pipeline, we discuss the role for verification and quality control in the increasingly complex life science workflows ushered in by synthetic biology.

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“…In 2017, Shipman et al (2017)successfully stored data in living cells. In 2018, Akhmetov et al (2018) proposed a long-term parallel storage of information in living cells. The method uses the pruning optimization algorithm.…”

Section: Introductionmentioning

confidence: 99%

High-density information storage and random access scheme using synthetic DNA

et al. 2021

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The high-storage density, long-life cycle, and low-energy consumption of DNA molecules make it the future of nextgeneration storage technology. However, DNA storage has the disadvantages of high-synthesis cost and low-random access efficiency. A high-density DNA-coding scheme can effectively reduce the cost of DNA synthesis. This paper first proposes a DNA-mapping method based on codebook and a random access method for DNA information based on encoded content. The mapping method satisfies the two biological constraints of homopolymer length and GC content. The random access method can efficiently and selectively read specific files in the DNA pool. To increase storage density, convolutional neural networks are combined with mapping methods to generate base sequences. In the experiments, our method was compared with the results of existing DNA information storage methods, which showed that the proposed scheme has better information storage density.

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A highly parallel strategy for storage of digital information in living cells

Cited by 5 publications

References 23 publications

Rapid, robust plasmid verification by de novo assembly of short sequencing reads

Rapid, robust plasmid verification by de novo assembly of short sequencing reads

Rapid, robust plasmid verification byde novoassembly of short sequencing reads

High-density information storage and random access scheme using synthetic DNA

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