%0 Generic
%A Cleij, Céline
%A Daran-Lapujade, Pascale
%A Danelon, Christophe
%D 2025
%T Data underlying chapter 4 of PhD thesis: Building the genome of a minimal synthetic cell
%U 
%R 10.4121/ad21c652-ad75-4a99-a09a-46c7d8f383d6.v1
%K Minimal synthetic cell
%K Synthetic genomics
%K Minimal genome
%K DNA assembly
%K Sacharomyces cerevisiae
%K Cell-free gene expression
%K PURE system
%X <p>This dataset belongs to the PhD thesis of Céline Cleij titled "Building the genome of a minimal synthetic cell".</p><p>Specifically, the dataset belongs to Chapter 4 titled "<em>De novo</em> design and assembly of minimal genomes for the synthetic cell".</p><p><br></p><p>Authors: Céline Cleij, Pascale Daran-Lapujade, Christophe Danelon</p><p>Corresponding authors: Pascale Daran-Lapujade and Christophe Danelon</p><p>Contact information: p.a.s.daran-lapujade@tudelft.nl and danelon@insa-toulouse.fr</p><p><br></p><p>This dataset contains data collected during experiments as part of Céline Cleij&#x27;s PhD project. The data was collected from 2023-2025.</p><p><br></p><p>All data processing and analysis steps are described in detail in the Methods section of thesis chapter 4.</p><p>Designed SynMG sequences (GenBank) were prepared with the SnapGene software, using the plasmid maps of the sequenced template plasmids and the designed primer sequences.</p><p>Raw Nanopore sequencing reads (fastq) were obtained by Plasmidsaurus (Eugene, OR, USA) using Nanopore sequencing technology.</p><p>Consensus SynMG sequences (GenBank) were obtained by Plasmidsaurus after processing of the raw reads, and were manually annotated in SnapGene.</p><p>The overview of relevant mutations ("Relevant mutations in SynMG variants") was prepared in Excel, based on mutations in consensus sequences and raw reads obtained from sequencing.</p><p>LC-MS data was obtained after processing in the Mascot software.</p><p><br></p><p><br></p><p>The data is grouped into seven files:</p><p>i) Designed SynMG sequences. Files are named after the SynMG version (SynMG1 or SynMG2).</p><p>ii) S. cerevisiae - Raw Nanopore sequencing reads. Files are named after the yeast strain from which total DNA was extracted, and after the SynMG variant which was assembled in this strain.</p><p>iii) S. cerevisiae - Consensus SynMG sequences. Files are named after the yeast strain from which total DNA was extracted, and after the SynMG variant which was assembled in this strain.</p><p>iv) E. coli - Raw Nanopore sequencing reads. Files are named after the E. coli strain from which SynChr DNA was extracted, and after the SynMG variant which was amplified in this strain.</p><p>v) E. coli - Consensus SynMG sequences. Files are named after the E. coli strain from which SynChr DNA was extracted, and after the SynMG variant which was amplified in this strain.</p><p>vi) Relevant mutations in SynMG variants. This Excel file contains an overview of all relevant mutations SynMG1.1, SynMG1.2, SynMG1.3, SynMG2.1 and SynMG2.2 compared to the designed maps.</p><p>vii) LC-MS data. This Excel file contains LC-MS data used for making Figure 4A, B &amp; D.</p><p><br></p>
%I 4TU.ResearchData