Data underlying the publication "Assembly and cell-free expression of a partial genome for the synthetic cell"

*** Assembly and cell-free expression of a partial genome for the synthetic cell ***<br>Authors: Céline Cleij, Laura Sierra Heras, Ellen Zwiers, 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 DanelonContact information: [e-mail] and [e-mail]<br>*** General introduction ***This dataset contains data collected during experiments for the manuscript "Assembly and cell-free expression of a partial genome for the synthetic cell". Data was collected in 2021-2025.<br>*** Methodological information ***Supplementary data 1-4 were prepared in Excel. The overview of relevant mutations in Supplementary data 4.5 is based on mutations in consensus sequences and raw reads obtained from sequencing.Supplementary data 5: Designed MSG sequences (GenBank) were prepared with the SnapGene software, using the plasmid maps of the sequenced template plasmids and the designed primer sequences.Supplementary data 6 and 7: Raw Nanopore sequencing reads (FASTQ) were obtained in house using Nanopore sequencing technology (for MSG0.1 and MSG0.2) or by Plasmidsaurus (Eugene, OR, USA) using Nanopore sequencing technology (for MSG1).Consensus SynChrs sequences (GenBank) for MSG0.1 and MSG0.2 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. Consensus sequences (GenBank) for MSG1 were obtained by Plasmidsaurus after processing of the raw reads, and were manually annotated in SnapGene.<br>All data processing and analysis steps are described in detail in the Methods section of the chapter.<br>*** Organization of the dataset ***See README file.

*** 合成细胞部分基因组的组装与无细胞表达 ***<br>作者：Céline Cleij、Laura Sierra Heras、Ellen Zwiers、Pascale Daran-Lapujade、Christophe Danelon<br>单位：代尔夫特理工大学（Delft University of Technology）生物纳米科学系、卡夫利纳米科学研究所（Kavli Institute of Nanoscience）；代尔夫特理工大学（Delft University of Technology）生物技术系；图卢兹生物技术研究所（TBI）、图卢兹大学（Université de Toulouse）、法国国家科研中心（CNRS）、法国国家农业食品与环境研究院（INRAE）、国立图卢兹应用科学学院（INSA）<br>通讯作者：Pascale Daran-Lapujade 与 Christophe Danelon<br>联系方式：[e-mail] 及 [e-mail]<br>*** 通用引言 ***<br>本数据集收录自论文《合成细胞部分基因组的组装与无细胞表达》相关实验的采集数据，数据采集时间为2021年至2025年。<br>*** 方法学说明 ***<br>补充数据1至4均以Excel格式编制。补充数据4.5中相关突变的概述，基于共有序列与测序获得的原始读段（raw reads）。<br>补充数据5：所设计的MSG序列（基因库格式，GenBank）通过SnapGene软件编制，所用素材为已测序的模板质粒的质粒图谱与设计好的引物序列。<br>补充数据6与7：原始纳米孔测序（Nanopore）读段（FASTQ格式），一部分由本实验室采用纳米孔测序技术获取（对应MSG0.1与MSG0.2），另一部分由美国俄勒冈州尤金市的Plasmidsaurus采用纳米孔测序技术获取（对应MSG1）。<br>MSG0.1与MSG0.2的共有SynChrs序列（基因库格式，GenBank），通过对经预处理的纳米孔测序读段采用Flye或Canu软件进行从头组装（de novo assembly）获得。若有必要，可结合Flye与Canu的组装结果及原始读段（raw reads）的信息，在SnapGene中对共有SynChrs序列进行组装。MSG1的共有序列（基因库格式，GenBank）由Plasmidsaurus在对原始读段（raw reads）进行预处理后获得，并在SnapGene中完成手动注释。<br>所有数据处理与分析步骤的详细说明，见该章节的方法部分。<br>*** 数据集组织方式 ***<br>详见README文件。