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Nat Commun. 2014 Sep 3;5:4767. doi: 10.1038/ncomms5767.

Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations.

Author information

1
1] Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent B-9052, Belgium [2] Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent B-9052, Belgium [3].
2
1] Unit for Medical Biotechnology, Inflammation Research Center, VIB, Technologiepark 927, Ghent B-9052, Belgium [2] Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, Ledeganckstraat 35, Ghent B-9052, Belgium [3].
3
1] Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, Ghent B-9000, Belgium [2] Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, Ghent B-9000, Belgium.
4
Center for Medical Genetics, Ghent University Hospital (MRB), De Pintelaan 185, Ghent B-9000, Belgium.
5
Bioinformatics Core Facility, Inflammation Research Center, VIB, Technologiepark 927, Ghent B-9052, Belgium.
6
1] Laboratory for Translational Genetics, Department of Oncology, KULeuven, Herestraat 49, Leuven B-3000, Belgium [2] Vesalius Research Center, VIB, Herestraat 49, Leuven B-3000, Belgium.
7
VIB BioInformatics Training and Services (BITS), Rijvisschestraat 120, Ghent B-9052, Belgium.
8
1] Complete Genomics Inc., 2071 Stierlin Court, Mountain View, California 94043, USA [2] BGI-Shenzhen, Building No. 11, Bei Shan Industrial Zone, Yantian District, Shenzhen 518083, China.
9
Complete Genomics Inc., 2071 Stierlin Court, Mountain View, California 94043, USA.
10
1] Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent B-9052, Belgium [2] Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent B-9052, Belgium [3] Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa.
11
1] Unit for Medical Biotechnology, Inflammation Research Center, VIB, Technologiepark 927, Ghent B-9052, Belgium [2] Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, Ledeganckstraat 35, Ghent B-9052, Belgium.

Abstract

The HEK293 human cell lineage is widely used in cell biology and biotechnology. Here we use whole-genome resequencing of six 293 cell lines to study the dynamics of this aneuploid genome in response to the manipulations used to generate common 293 cell derivatives, such as transformation and stable clone generation (293T); suspension growth adaptation (293S); and cytotoxic lectin selection (293SG). Remarkably, we observe that copy number alteration detection could identify the genomic region that enabled cell survival under selective conditions (i.c. ricin selection). Furthermore, we present methods to detect human/vector genome breakpoints and a user-friendly visualization tool for the 293 genome data. We also establish that the genome structure composition is in steady state for most of these cell lines when standard cell culturing conditions are used. This resource enables novel and more informed studies with 293 cells, and we will distribute the sequenced cell lines to this effect.

PMID:
25182477
PMCID:
PMC4166678
DOI:
10.1038/ncomms5767
[Indexed for MEDLINE]
Free PMC Article

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