Data underlying chapter 3 of PhD thesis: Building the genome of a minimal synthetic cell
DOI: 10.4121/feb7423b-8194-4d99-89d8-593023e06473
Datacite citation style
Dataset
Licence CC BY-NC 4.0
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".
Authors: Céline Cleij, Pascale Daran-Lapujade, Christophe Danelon
Corresponding authors: Pascale Daran-Lapujade and Christophe Danelon
Contact information: [email protected] and [email protected]
This dataset contains data collected during experiments as part of Céline Cleij's PhD project. The data was collected from 2021-2025.
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.
All data processing and analysis steps are described in detail in the Methods section of the publication.
The data is grouped into three zip files:
i) 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.
ii) 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.
iii) Designed SynChr sequences
Files are named after the SynChr version (SynChr_control, SynChr_PURE, SynChr_control_2mu, SynChr_PURE_2mu).
History
- 2025-03-27 first online, published, posted
Publisher
4TU.ResearchDataFormat
Raw Nanopore sequencing reads/fastq; Consensus SynChr sequences/GenBank; Designed SynChr sequences/GenBankFunding
- BaSyC – Building a Synthetic Cell Gravitation grant (grant code 024.003.019) NWO
- ANR grant (grant code ANR-22-CPJ2-0091-01) Agence Nationale de la Recherche
Organizations
Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology;Faculty of Applied Sciences, Department of Biotechnology, Delft University of Technology;
Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA
DATA
Files (4)
- 2,344 bytesMD5:
44ee40698a128b7c6d77a6f8b94b5252
README.txt - 283,274 bytesMD5:
488a8dedcc7a0861acaf5fddb8be5dca
Consensus SynChr sequences.zip - 128,975 bytesMD5:
43dec3104f9dafc11d08220f3ea70eb2
Designed SynChr sequences.zip - 7,857,976,550 bytesMD5:
8a42c8455e6334dfa81b1a9010a08a2d
Raw Nanopore sequencing reads.zip -
download all files (zip)
7,858,391,143 bytes unzipped