title: Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations.
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.
authors.affiliation: 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].
authors.forename: Yao-Cheng
authors.initials: YC
authors.lastname: Lin
authors.affiliation: 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].
authors.forename: Morgane
authors.initials: M
authors.lastname: Boone
authors.affiliation: 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].
authors.forename: Leander
authors.initials: L
authors.lastname: Meuris
authors.affiliation: 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.
authors.forename: Irma
authors.initials: I
authors.lastname: Lemmens
authors.affiliation: Center for Medical Genetics, Ghent University Hospital (MRB), De Pintelaan 185, Ghent B-9000, Belgium.
authors.forename: Nadine
authors.initials: N
authors.lastname: Van Roy
authors.affiliation: Bioinformatics Core Facility, Inflammation Research Center, VIB, Technologiepark 927, Ghent B-9052, Belgium.
authors.forename: Arne
authors.initials: A
authors.lastname: Soete
authors.affiliation: 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.
authors.forename: Joke
authors.initials: J
authors.lastname: Reumers
authors.affiliation: 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.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Moisse
authors.affiliation: VIB BioInformatics Training and Services (BITS), Rijvisschestraat 120, Ghent B-9052, Belgium.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Plaisance
authors.affiliation: 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.
authors.forename: Radoje
authors.initials: R
authors.lastname: Drmanac
authors.affiliation: Complete Genomics Inc., 2071 Stierlin Court, Mountain View, California 94043, USA.
authors.forename: Jason
authors.initials: J
authors.lastname: Chen
authors.affiliation: Center for Medical Genetics, Ghent University Hospital (MRB), De Pintelaan 185, Ghent B-9000, Belgium.
authors.forename: Frank
authors.initials: F
authors.lastname: Speleman
authors.affiliation: 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.
authors.forename: Diether
authors.initials: D
authors.lastname: Lambrechts
authors.affiliation: 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.
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.affiliation: 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.
authors.forename: Jan
authors.initials: J
authors.lastname: Tavernier
authors.affiliation: 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.
authors.forename: Nico
authors.initials: N
authors.lastname: Callewaert
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D001483:Base Sequence; D049109:Cell Proliferation; D002470:Cell Survival / Q000235:genetics; D002999:Clone Cells; D015925:Cryopreservation; D056915:DNA Copy Number Variations; D020869:Gene Expression Profiling; D015894:Genome, Human; D042822:Genomic Instability; D057809:HEK293 Cells; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D059785:Karyotype; D008969:Molecular Sequence Data; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism; D059467:Transcriptome; D014170:Transformation, Genetic