Data underlying the publication "Assembly and cell-free expression of a partial genome for the synthetic cell"

DOI:10.4121/4eb28eac-b94c-4e97-9db6-4cd3af73fad2.v1
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DOI: 10.4121/4eb28eac-b94c-4e97-9db6-4cd3af73fad2

Datacite citation style

Cleij, Céline; Sierra Heras, Laura; Zwiers, Ellen; Pascale Daran-Lapujade; Danelon, Christophe (2025): Data underlying the publication "Assembly and cell-free expression of a partial genome for the synthetic cell". Version 1. 4TU.ResearchData. dataset. https://doi.org/10.4121/4eb28eac-b94c-4e97-9db6-4cd3af73fad2.v1
Other citation styles (APA, Harvard, MLA, Vancouver, Chicago, IEEE) available at Datacite

Dataset

*** Assembly and cell-free expression of a partial genome for the synthetic cell ***


Authors: Céline Cleij, Laura Sierra Heras, Ellen Zwiers, Pascale Daran-Lapujade, Christophe Danelon

Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology;

Department of Biotechnology, Delft University of Technology;

Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA


Corresponding authors: Pascale Daran-Lapujade and Christophe Danelon

Contact information: p.a.s.daran-lapujade@tudelft.nl and danelon@insa-toulouse.fr


*** General introduction ***

This dataset contains data collected during experiments for the manuscript "Assembly and cell-free expression of a partial genome for the synthetic cell". Data was collected in 2021-2025.


*** Methodological information ***

Supplementary data 1-4 were prepared in Excel. The overview of relevant mutations in Supplementary data 4.5 is based on mutations in consensus sequences and raw reads obtained from sequencing.

Supplementary data 5: Designed MSG sequences (GenBank) were prepared with the SnapGene software, using the plasmid maps of the sequenced template plasmids and the designed primer sequences.

Supplementary data 6 and 7: Raw Nanopore sequencing reads (FASTQ) were obtained in house using Nanopore sequencing technology (for MSG0.1 and MSG0.2) or by Plasmidsaurus (Eugene, OR, USA) using Nanopore sequencing technology (for MSG1).

Consensus SynChrs sequences (GenBank) for MSG0.1 and MSG0.2 were obtained after de novo assembly of the processed Nanopore sequencing reads using Flye or Canu. If necessary, a consensus SynChr sequence was assembled in SnapGene using information from the Flye and Canu assemblies and raw reads. Consensus sequences (GenBank) for MSG1 were obtained by Plasmidsaurus after processing of the raw reads, and were manually annotated in SnapGene.


All data processing and analysis steps are described in detail in the Methods section of the chapter.


*** Organization of the dataset ***

See README file.

History

  • 2025-10-06 first online, published, posted

Publisher

4TU.ResearchData

Format

Supplementary data 1-4/Excel; Supplementary data 5 Designed sequences/GenBank; Supplementary data 6 & 7 Consensus sequences/GenBank; Supplementary data 6 & 7 Raw reads/FASTQ

Funding

  • BaSyC – Building a Synthetic Cell Gravitation grant (grant code 024.003.019) NWO
  • ANR grant (grant code ANR-22-CPJ2-0091-01) Agence Nationale de la Recherche

Organizations

Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology
TU Delft, Faculty of Applied Sciences, Department of Biotechnology
Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA

DATA

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