All Publications

  • High density DNA data storage library via dehydration with digital microfluidic retrieval. Nature communications Newman, S., Stephenson, A. P., Willsey, M., Nguyen, B. H., Takahashi, C. N., Strauss, K., Ceze, L. 2019; 10 (1): 1706


    DNA promises to be a high density data storage medium, but physical storage poses a challenge. To store large amounts of data, pools must be physically isolated so they can share the same addressing scheme. We propose the storage of dehydrated DNA spots on glass as an approach for scalable DNA data storage. The dried spots can then be retrieved by a water droplet using a digital microfluidic device. Here we show that this storage schema works with varying spot organization, spotted masses of DNA, and droplet retrieval dwell times. In all cases, the majority of the DNA was retrieved and successfully sequenced. We demonstrate that the spots can be densely arranged on a microfluidic device without significant contamination of the retrieval. We also demonstrate that 1TB of data could be stored in a single spot of DNA and successfully retrieved using this method.

    View details for PubMedID 30979873

  • Puddle: A Dynamic, Error-Correcting, Full-Stack Microfluidics Platform Willsey, M., Stephenson, A. P., Takahashi, C., Vaid, P., Nguyen, B. H., Piszczek, M., Betts, C., Newman, S., Joshi, S., Strauss, K., Ceze, L., ACM ASSOC COMPUTING MACHINERY. 2019: 183–97
  • Random access in large-scale DNA data storage NATURE BIOTECHNOLOGY Organick, L., Ang, S., Chen, Y., Lopez, R., Yekhanin, S., Makarychev, K., Racz, M. Z., Kamath, G., Gopalan, P., Nguyen, B., Takahashi, C. N., Newman, S., Parker, H., Rashtchian, C., Stewart, K., Gupta, G., Carlson, R., Mulligan, J., Carmean, D., Seelig, G., Ceze, L., Strauss, K. 2018; 36 (3): 242-+


    Synthetic DNA is durable and can encode digital data with high density, making it an attractive medium for data storage. However, recovering stored data on a large-scale currently requires all the DNA in a pool to be sequenced, even if only a subset of the information needs to be extracted. Here, we encode and store 35 distinct files (over 200 MB of data), in more than 13 million DNA oligonucleotides, and show that we can recover each file individually and with no errors, using a random access approach. We design and validate a large library of primers that enable individual recovery of all files stored within the DNA. We also develop an algorithm that greatly reduces the sequencing read coverage required for error-free decoding by maximizing information from all sequence reads. These advances demonstrate a viable, large-scale system for DNA data storage and retrieval.

    View details for DOI 10.1038/nbt.4079

    View details for Web of Science ID 000426698700018

    View details for PubMedID 29457795