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

Yao-Cheng Lin (UGent) , Morgane Boone (UGent) , Leander Meuris (UGent) , Irma Lemmens (UGent) , Nadine Van Roy (UGent) , Arne Soete (UGent) , Joke Reumers, Matthieu Moisse, Stéphane Plaisance (UGent) , Radoje Drmanac, et al.
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Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
LRP1B, MUTATIONS, STABILITY, DNA, GENE, ADENOVIRUS, EXPRESSION, RENAL-CANCER, FUMARATE HYDRATASE, TUMOR-SUPPRESSOR

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Chicago
Lin, Yao-Cheng, Morgane Boone, Leander Meuris, Irma Lemmens, Nadine Van Roy, Arne Soete, Joke Reumers, et al. 2014. “Genome Dynamics of the Human Embryonic Kidney 293 Lineage in Response to Cell Biology Manipulations.” Nature Communications 5.
APA
Lin, Y.-C., Boone, M., Meuris, L., Lemmens, I., Van Roy, N., Soete, A., Reumers, J., et al. (2014). Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations. NATURE COMMUNICATIONS, 5.
Vancouver
1.
Lin Y-C, Boone M, Meuris L, Lemmens I, Van Roy N, Soete A, et al. Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations. NATURE COMMUNICATIONS. 2014;5.
MLA
Lin, Yao-Cheng, Morgane Boone, Leander Meuris, et al. “Genome Dynamics of the Human Embryonic Kidney 293 Lineage in Response to Cell Biology Manipulations.” NATURE COMMUNICATIONS 5 (2014): n. pag. Print.
@article{5753022,
  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.},
  articleno    = {4767},
  author       = {Lin, Yao-Cheng and Boone, Morgane and Meuris, Leander and Lemmens, Irma and Van Roy, Nadine and Soete, Arne and Reumers, Joke and Moisse, Matthieu and Plaisance, St{\'e}phane and Drmanac, Radoje and Chen, Jason and Speleman, Franki and Lambrechts, Diether and Van de Peer, Yves and Tavernier, Jan and Callewaert, Nico},
  issn         = {2041-1723},
  journal      = {NATURE COMMUNICATIONS},
  keyword      = {LRP1B,MUTATIONS,STABILITY,DNA,GENE,ADENOVIRUS,EXPRESSION,RENAL-CANCER,FUMARATE HYDRATASE,TUMOR-SUPPRESSOR},
  language     = {eng},
  pages        = {12},
  title        = {Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations},
  url          = {http://dx.doi.org/10.1038/ncomms5767},
  volume       = {5},
  year         = {2014},
}

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