cff-version: 1.2.0
abstract: "<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 3 titled "Synthetic chromosome assembly in yeast for cell-free protein synthesis".</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 2021-2025.</p><p><br></p><p>Raw Nanopore sequencing reads (fastq) were obtained in-house using MinION technology (Oxford Nanopore Technologies, Oxford, UK).</p><p>Consensus SynChrs sequences (GenBank) 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.</p><p>Designed SynChr sequences (GenBank) were prepared using SnapGene, using the plasmid maps of the sequenced template plasmids and the designed primer sequences.</p><p><br></p><p>All data processing and analysis steps are described in detail in the Methods section of the publication.</p><p><br></p><p>The data is grouped into three zip files:</p><p>i) Raw Nanopore sequencing reads</p><p>Files are named after the yeast strain from which total DNA was extracted. For IMF51 and IMF54, raw reads of the second sequencing run are deposited.</p><p><br></p><p>ii) Consensus SynChr sequences</p><p>Files are named after the yeast strain from which total DNA was extracted, and after the SynChr version (SynChr_control or SynChr_PURE) which was assembled in this strain.</p><p><br></p><p>iii) Designed SynChr sequences</p><p>Files are named after the SynChr version (SynChr_control, SynChr_PURE, SynChr_control_2mu, SynChr_PURE_2mu).</p>"
authors:
  - family-names: Cleij
    given-names: Céline
    orcid: "https://orcid.org/0000-0001-6580-1106"
  - family-names: Daran-Lapujade
    given-names: Pascale
    orcid: "https://orcid.org/0000-0002-4097-7831"
  - family-names: Danelon
    given-names: Christophe
title: "Data underlying chapter 3 of PhD thesis: Building the genome of a minimal synthetic cell"
keywords:
version: 1
identifiers:
  - type: doi
    value: 10.4121/feb7423b-8194-4d99-89d8-593023e06473.v1
license: CC BY-NC 4.0
date-released: 2025-03-27