EIC01-01-1280 | Sequencing Runs from Motif-based DNA Data Storage Systems

Helixworks has developed a novel DNA data storage method that encodes digital information using composite motifs - short, predefined DNA sequences assembled in specific orders. Unlike base-by-base synthesis, this approach uses enzymatic ligation of DNA building blocks (called motifs), allowing for high-throughput, cost-efficient synthesis with built-in error tolerance.

Each oligo in the storage pool contains a structured arrangement of addressing barcodes, primers, and payload motifs, enabling robust multiplexing and retrieval. Information is read out via Oxford Nanopore sequencing and decoded by identifying the motifs present in each read. This architecture supports scalable, high-density molecular storage and can be integrated with automated workflows for synthesis and sequencing.

This dataset contains raw and processed outputs from a Helixworks composite motif-based DNA data storage experiment. Each archive includes:

Raw signal-level sequencing data (FAST5) – Generated via Oxford Nanopore sequencing (R10.4.1 / FLO-MIN114) of synthetic oligos assembled using Helixworks’ composite motif ligation protocol.

Design file (*_encoded.tsv) – Lists the intended motif sequence per oligo, including barcode and primer motifs, which define the structure and payload mapping.

Zero-error motif alignment file (*_master_db.txt) – Captures high-confidence motif alignments per read with no substitution, insertion, or deletion errors. Each row follows the format: [read_id] [filename] [barcode_id] [strand] [start] [end] [motif_id] [row_index] [column_index]

Used to validate motif calling accuracy and reconstruct encoded payloads from sequencing reads.
A detailed description of the oligo architecture, including inner address and outer barcode arrangement, primer locations, and motif layout can be found in the linked OSF DOI.

Experimental Condition
ONT Barcodes (Outer Barcodes)
DNA amount loaded into the Flow Cell

EIC01-01-1280-T1
NB01, NB05, NB09, NB13, NB17, NB21, NB25, NB29, NB33, NB37, NB41, NB45, NB49, NB53, NB57, NB61, NB65, NB69, NB73, NB77
32.470 amol / HW Address

EIC01-01-1280-T2
NB02, NB06, NB10, NB14, NB18, NB22, NB26, NB30, NB34, NB38, NB42, NB46, NB50, NB54, NB58, NB62, NB66, NB70, NB74, NB78
1.0670 amol / HW Address

EIC01-01-1280-T3
NB03, NB07, NB11, NB15, NB19, NB23, NB27, NB31, NB35, NB39, NB43, NB47, NB51, NB55, NB59, NB63, NB67, NB71, NB75, NB79
0.4363 amol / HW Address

EIC01-01-1280-T4
NB04, NB08, NB12, NB16, NB20, NB24, NB28, NB32, NB36, NB40, NB44, NB48, NB52, NB56, NB60, NB64, NB68, NB72, NB76, NB80
0.1091 amol / HW Address

ONT Barcodes:

Unique set of 20 Barcodes from Oxford Nanopore Technologies (ONT) used for Outer Addressing of a pool of 64 HW_Address Oligos

DNA amount loaded into the Flow Cell:

represents the amount of DNA (in Attomole) loaded into the MinION flow cell per each HW Address of the 1280-well synthesis.