Data underlying the publication: MOSAIC: a highly efficient, one-step recombineering approach to plasmid editing and diversification

DOI:10.4121/4464ab86-9214-49b3-a808-10ca655385a6.v4
The DOI displayed above is for this specific version of this dataset, which is currently the latest. Newer versions may be published in the future. For a link that will always point to the latest version, please use
DOI: 10.4121/4464ab86-9214-49b3-a808-10ca655385a6
Datacite citation style:
van den Brink, Marijn; Althuis, Timotheus; Danelon, Christophe; Claassens, Nico (2025): Data underlying the publication: MOSAIC: a highly efficient, one-step recombineering approach to plasmid editing and diversification. Version 4. 4TU.ResearchData. dataset. https://doi.org/10.4121/4464ab86-9214-49b3-a808-10ca655385a6.v4
Other citation styles (APA, Harvard, MLA, Vancouver, Chicago, IEEE) available at Datacite

Dataset

choose version:
version 4 - 2025-02-03 (latest)
version 3 - 2024-09-24 version 2 - 2024-03-25 version 1 - 2024-03-14
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Usage statistics

221
views
511
downloads

Geolocation

the Netherlands

Time coverage

2022-2024

Licence

CC BY 4.0

Data underlying the pre-print: Van den Brink, M., Althuis, T.Y., Danelon, C. and Claassens, N.J. (2024) MOSAIC: a highly efficient, one-step recombineering approach to plasmid editing and diversification. bioRxiv, 10.1101/2024.03.22.586135.


This dataset contains data collected during experiments as part of Marijn van den Brink's and Timotheus Althuis' PhD projects. The raw data consists of Nanopore sequencing data. Nanopore sequencing was performed by Plasmidsaurus (Oregon, US). The FASTQ files were then mapped to reference sequences, resulting in .bam/.bai files. These were further analyzed using an in-house developed R script. All data processing and analysis steps are described in detail in the methods section of the publication.


The data is grouped in folders based on the figures in the publication. The folder name specifies the figure number and contains a short description of the data. Each folder contains raw data (FASTQ) and processed data. The processed data consists of (i) the mapped reads (file format: .bam and .bai), (ii) the analysis results of the mapped reads (file format: .csv and .xlsx), (iii) the graphs plotting the results (file format: .pzfx), and (iv) the R scripts used to produce the results incl. the required .xlsx or .csv files.


To analyze your own data using our R script, go to "General Nanopore data analysis scripts > MOSAIC-library-analysis-script.R". This R script contains information on how to adapt the script to your own data.

History

  • 2024-03-14 first online
  • 2025-02-03 published, posted

Publisher

4TU.ResearchData

Format

Nanopore sequencing reads/fastq; aligned sequences/BAM; analyzed results/csv; graphs/pzfx; analysis code/R

Funding

  • BaSyC – Building a Synthetic Cell Gravitation grant (grant code 024.003.019) NWO
  • XL (grant code OCENW.XL21.XL21.007) NWO
  • Veni Fellowship (grant code VI.Veni.192.156) NWO
  • (grant code ANR-22-CPJ2-0091-01) Agence nationale de la recherche

Organizations

Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology;
Laboratory of Microbiology, Wageningen University;
Toulouse Biotechnology Institute (TBI), Université de Toulouse

DATA

Files (5)