van den Brink, Marijn; Althuis, Timotheus; Danelon, Christophe; Claassens, Nico (2024): Data underlying the publication: MOSAIC: a highly efficient, one-step recombineering approach to plasmid editing and diversification. Version 2. 4TU.ResearchData. dataset. https://doi.org/10.4121/4464ab86-9214-49b3-a808-10ca655385a6.v2

Dataset

x choose version: version 3 - 2024-09-24 (latest) version 1 - 2024-03-14

• Microbiology
• Genetics
• Biological Sciences

combinatorial libraries, MAGE, multiplex, Nanopore sequencing, plasmid libraries, recombineering

2022-2024

CC BY 4.0

RefWorks, BibTeX, Reference Manager, Endnote, DataCite, NLM, DC, CFF

by Marijn van den Brink , Timotheus Althuis , Christophe Danelon , Nico Claassens

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 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.

• 2024-03-14 first online

• 2024-03-25 published, posted

4TU.ResearchData

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

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

• 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
• ANR pour Chaire Professeur Junior (grant code ANR-2023-004) Agence nationale de la recherche

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