Data underlying chapter 4 of PhD thesis: Building the genome of a minimal synthetic cell

This dataset belongs to the PhD thesis of Céline Cleij titled "Building the genome of a minimal synthetic cell".Specifically, the dataset belongs to Chapter 4 titled "<em>De novo</em> design and assembly of minimal genomes for the synthetic cell".<br>Authors: Céline Cleij, Pascale Daran-Lapujade, Christophe DanelonCorresponding authors: Pascale Daran-Lapujade and Christophe DanelonContact information: [e-mail] and [e-mail]<br>This dataset contains data collected during experiments as part of Céline Cleij's PhD project. The data was collected from 2023-2025.<br>All data processing and analysis steps are described in detail in the Methods section of thesis chapter 4.Designed SynMG sequences (GenBank) were prepared with the SnapGene software, using the plasmid maps of the sequenced template plasmids and the designed primer sequences.Raw Nanopore sequencing reads (fastq) were obtained by Plasmidsaurus (Eugene, OR, USA) using Nanopore sequencing technology.Consensus SynMG sequences (GenBank) were obtained by Plasmidsaurus after processing of the raw reads, and were manually annotated in SnapGene.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.LC-MS data was obtained after processing in the Mascot software.The tables S4.1-S4.15 were prepared in Excel. <br><br>The data is grouped into eight files: <br>i) Zip file "Designed SynMG sequences"Files are named after the SynMG version (SynMG1 or SynMG2).<br>ii) Zip file "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.<br>iii) Zip file "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.<br>iv) Zip file "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.<br>v) Zip file "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.<br>vi) Excel file "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. <br>vii) Excel file "LC-MS data"This Excel file contains LC-MS data used for making Figure 4A, B &amp; D.<br>viii) Excel file "Tables S4.1-S4.15"This Excel file contains the supplementary tables S4.1 to S4.15, which contain information about all used strains, synthetic chromosomes, plasmids, primers and SHRs used in this study.<br>

本数据集隶属于Céline Cleij题为“构建最小合成细胞基因组”的博士学位论文，具体属于第四章《最小合成细胞基因组的从头（de novo）设计与组装》。

作者：Céline Cleij、Pascale Daran-Lapujade、Christophe Danelon；通讯作者为Pascale Daran-Lapujade与Christophe Danelon，联系方式为[e-mail]及[e-mail]。

本数据集包含Céline Cleij博士研究项目中实验采集的相关数据，数据采集周期为2023年至2025年。所有数据处理与分析步骤均在该论文第四章的方法部分有详细阐述。

设计的SynMG序列（GenBank格式）通过SnapGene软件制备，所用模板为已测序的质粒图谱与设计的引物序列。原始纳米孔（Nanopore）测序读数（FASTQ格式）由美国俄勒冈州尤金市的Plasmidsaurus公司采用纳米孔测序技术获取。经原始读数处理后得到的共识SynMG序列（GenBank格式）由Plasmidsaurus生成，并通过SnapGene进行人工注释。基于测序得到的共识序列与原始读数，在Excel中整理得到了“SynMG变异体相关突变”概览表。液相色谱-质谱联用（LC-MS）数据经Mascot软件处理后获得。补充表S4.1至S4.15均通过Excel编制完成。

本数据集共分为8个文件组：
i) 压缩包“设计的SynMG序列”：文件以SynMG版本（SynMG1或SynMG2）命名。
ii) 压缩包“酿酒酵母（S. cerevisiae）- 原始纳米孔测序读数”：文件以提取总DNA的酵母菌株，以及在该菌株中组装的SynMG变异体命名。
iii) 压缩包“酿酒酵母（S. cerevisiae）- 共识SynMG序列”：文件以提取总DNA的酵母菌株，以及在该菌株中组装的SynMG变异体命名。
iv) 压缩包“大肠杆菌（E. coli）- 原始纳米孔测序读数”：文件以提取SynChr DNA的大肠杆菌菌株，以及在该菌株中扩增的SynMG变异体命名。
v) 压缩包“大肠杆菌（E. coli）- 共识SynMG序列”：文件以提取SynChr DNA的大肠杆菌菌株，以及在该菌株中扩增的SynMG变异体命名。
vi) Excel文件“SynMG变异体相关突变”：该Excel文件包含了SynMG1.1、SynMG1.2、SynMG1.3、SynMG2.1及SynMG2.2相较于设计图谱的全部相关突变概览。
vii) Excel文件“LC-MS数据”：该Excel文件包含用于绘制图4A、B及D的液相色谱-质谱联用数据。
viii) Excel文件“表S4.1-S4.15”：该Excel文件包含补充表S4.1至S4.15，其中收录了本研究中所用全部菌株、合成染色体、质粒、引物及SHRs的相关信息。