Data underlying chapter 3 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 3 titled "Synthetic chromosome assembly in yeast for cell-free protein synthesis".<br>Authors: Céline Cleij, Pascale Daran-Lapujade, Christophe DanelonDepartment of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology;Department of Biotechnology, Delft University of Technology;Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA<br>Corresponding authors: Pascale Daran-Lapujade and Christophe Danelon<br>Contact information: [e-mail] and [e-mail]<br><br>*** General introduction ***This dataset contains data collected during experiments as part of Céline Cleij's PhD project. The data was collected from 2021-2025.<br><br>*** Methodological information ***Raw Nanopore sequencing reads (fastq) were obtained in-house using MinION technology (Oxford Nanopore Technologies, Oxford, UK).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.Designed SynChr sequences (GenBank) were prepared using SnapGene, using the plasmid maps of the sequenced template plasmids and the designed primer sequences.Tables S3.1-S3.17 were prepared in Excel.<br>All data processing and analysis steps are described in detail in the Methods section of the publication.<br><br>*** Organization of the dataset ***The data is grouped into four files:<br>i) Zip file "Raw Nanopore sequencing reads"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.<br>ii) Zip file "Consensus SynChr sequences"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.<br>iii) Zip file "Designed SynChr sequences"Files are named after the SynChr version (SynChr_control, SynChr_PURE, SynChr_control_2mu, SynChr_PURE_2mu).<br>iv) Excel file "Tables S3.1-S3.17"This Excel file contains the supplementary tables S3.1 to S3.17, which contain information about all used strains, synthetic chromosomes, plasmids, primers and SHRs used in this study.

本数据集隶属于西琳·克莱伊（Céline Cleij）题为《构建最小合成细胞基因组》的博士学位论文，具体属于第三章《用于无细胞蛋白合成的酵母合成染色体组装》。
作者：西琳·克莱伊、帕斯卡尔·达朗-拉普雅德、克里斯托夫·达内隆
单位：代尔夫特理工大学卡夫利纳米科学研究所生物纳米科学系；代尔夫特理工大学生物技术系；图卢兹大学图卢兹生物技术研究所（TBI），法国国家科学研究中心（CNRS）、法国国家农业食品与环境研究院（INRAE）、图卢兹国立应用科学学院（INSA）
通讯作者：帕斯卡尔·达朗-拉普雅德与克里斯托夫·达内隆
联系方式：[e-mail] 与 [e-mail]

*** 通用引言 ***
本数据集包含西琳·克莱伊博士研究项目中实验采集的数据，采集周期为2021年至2025年。

*** 方法学信息 ***
原始Nanopore测序读段（fastq）由本课题组使用MinION技术（Oxford Nanopore Technologies，英国牛津）获取。经处理的Nanopore测序读段通过Flye或Canu工具进行从头组装后，得到合成染色体（SynChrs）序列（GenBank格式）。若有必要，可结合Flye与Canu组装结果及原始读段信息，在SnapGene中组装得到合成染色体的共识序列。
设计的合成染色体序列（GenBank格式）通过SnapGene制备，所用参考信息为已测序模板质粒的质粒图谱与设计的引物序列。
辅助表S3.1~S3.17通过Excel软件制作。
所有数据处理与分析步骤的详细说明见该研究论文的方法学章节。

*** 数据集组织方式 ***
本数据集分为四个文件组：
i) 压缩包"原始Nanopore测序读段"：文件以提取总DNA的酵母菌株命名，其中IMF51与IMF54菌株包含第二轮测序的原始读段。
ii) 压缩包"合成染色体共识序列"：文件以提取总DNA的酵母菌株及该菌株中组装的合成染色体版本（SynChr_control或SynChr_PURE）命名。
iii) 压缩包"设计的合成染色体序列"：文件以合成染色体版本命名，包括SynChr_control、SynChr_PURE、SynChr_control_2mu、SynChr_PURE_2mu。
iv) Excel文件"Tables S3.1-S3.17"：该Excel文件包含补充表S3.1至S3.17，其中记录了本研究中使用的所有菌株、合成染色体、质粒、引物以及同源重组序列（SHRs）的相关信息。