Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing

Becker J, Hackel M, Jakobi T, Rupp O, Schneider J, Szczepanowski R, Bekel T, Borth N, Goesmann A, Grillari J, Kaltschmidt C, et al. (2011)
Journal of Biotechnology 156(3): 227-235.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
The pyrosequencing technology from 454 Life Sciences and a novel assembly approach for cDNA sequences with the Newbler Assembler were used to achieve a major step forward to unravel the transcriptome of Chinese hamster ovary (CHO) cells. Normalized cDNA libraries originating from several cell lines and diverse culture conditions were sequenced and the resulting 1.84 million reads were assembled into 32,801 contiguous sequences, 29,184 isotigs, and 24,576 isogroups. A taxonomic classification of the isotigs showed that more than 70% of the assembled data is most similar to the transcriptome of Mus musculus, with most of the remaining isotigs being homologous to DNA sequences from Rattus norvegicus. Mapping of the CHO cell line contigs to the mouse transcriptome demonstrated that 9124 mouse transcripts, representing 6701 genes, are covered by more than 95% of their sequence length. Metabolic pathways of the central carbohydrate metabolism and biosynthesis routes of sugars used for protein N-glycosylation were reconstructed from the transcriptome data. All relevant genes representing major steps in the N-glycosylation pathway of CHO cells were detected. The present manuscript represents a data set of assembled and annotated genes for CHO cells that can now be used for a detailed analysis of the molecular functioning of CHO cell lines.
Journal of Biotechnology
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Becker J, Hackel M, Jakobi T, et al. Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. Journal of Biotechnology. 2011;156(3):227-235.
Becker, J., Hackel, M., Jakobi, T., Rupp, O., Schneider, J., Szczepanowski, R., Bekel, T., et al. (2011). Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. Journal of Biotechnology, 156(3), 227-235. https://doi.org/10.1016/j.jbiotec.2011.09.014
Becker, J., Hackel, M., Jakobi, T., Rupp, O., Schneider, J., Szczepanowski, R., Bekel, T., Borth, N., Goesmann, A., Grillari, J., et al. (2011). Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. Journal of Biotechnology 156, 227-235.
Becker, J., et al., 2011. Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. Journal of Biotechnology, 156(3), p 227-235.
J. Becker, et al., “Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing”, Journal of Biotechnology, vol. 156, 2011, pp. 227-235.
Becker, J., Hackel, M., Jakobi, T., Rupp, O., Schneider, J., Szczepanowski, R., Bekel, T., Borth, N., Goesmann, A., Grillari, J., Kaltschmidt, C., Noll, T., Pühler, A., Tauch, A., Brinkrolf, K.: Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. Journal of Biotechnology. 156, 227-235 (2011).
Becker, Jennifer, Hackel, M, Jakobi, Tobias, Rupp, Oliver, Schneider, Jessica, Szczepanowski, Rafael, Bekel, Thomas, Borth, N, Goesmann, Alexander, Grillari, J, Kaltschmidt, Christian, Noll, Thomas, Pühler, Alfred, Tauch, Andreas, and Brinkrolf, Karina. “Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing”. Journal of Biotechnology 156.3 (2011): 227-235.

48 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

A cross-species whole genome siRNA screen in suspension-cultured Chinese hamster ovary cells identifies novel engineering targets.
Klanert G, Fernandez DJ, Weinguny M, Eisenhut P, Bühler E, Melcher M, Titus SA, Diendorfer AB, Gludovacz E, Jadhav V, Xiao S, Stern B, Lal M, Shiloach J, Borth N., Sci Rep 9(1), 2019
PMID: 31213643
CHO-Omics Review: The Impact of Current and Emerging Technologies on Chinese Hamster Ovary Based Bioproduction.
Stolfa G, Smonskey MT, Boniface R, Hachmann AB, Gulde P, Joshi AD, Pierce AP, Jacobia SJ, Campbell A., Biotechnol J 13(3), 2018
PMID: 29072373
Glycoengineering in CHO Cells: Advances in Systems Biology.
Tejwani V, Andersen MR, Nam JH, Sharfstein ST., Biotechnol J 13(3), 2018
PMID: 29316325
Integrative analysis of DNA methylation and gene expression in butyrate-treated CHO cells.
Wippermann A, Rupp O, Brinkrolf K, Hoffrogge R, Noll T., J Biotechnol 257(), 2017
PMID: 27890772
What can mathematical modelling say about CHO metabolism and protein glycosylation?
Galleguillos SN, Ruckerbauer D, Gerstl MP, Borth N, Hanscho M, Zanghellini J., Comput Struct Biotechnol J 15(), 2017
PMID: 28228925
Therapeutic glycoprotein production in mammalian cells.
Lalonde ME, Durocher Y., J Biotechnol 251(), 2017
PMID: 28465209
The use of 'Omics technology to rationally improve industrial mammalian cell line performance.
Lewis AM, Abu-Absi NR, Borys MC, Li ZJ., Biotechnol Bioeng 113(1), 2016
PMID: 26059229
Genetic analysis of the clonal stability of Chinese hamster ovary cells for recombinant protein production.
Li H, Chen K, Wang Z, Li D, Lin J, Yu C, Yu F, Wang X, Huang L, Jiang C, Gu H, Fang J., Mol Biosyst 12(1), 2016
PMID: 26563441
Effect of Temperature Downshift on the Transcriptomic Responses of Chinese Hamster Ovary Cells Using Recombinant Human Tissue Plasminogen Activator Production Culture.
Bedoya-López A, Estrada K, Sanchez-Flores A, Ramírez OT, Altamirano C, Segovia L, Miranda-Ríos J, Trujillo-Roldán MA, Valdez-Cruz NA., PLoS One 11(3), 2016
PMID: 26991106
Sequencing technologies for animal cell culture research.
Kremkow BG, Lee KH., Biotechnol Lett 37(1), 2015
PMID: 25214225
Global insights into the Chinese hamster and CHO cell transcriptomes.
Vishwanathan N, Yongky A, Johnson KC, Fu HY, Jacob NM, Le H, Yusufi FN, Lee DY, Hu WS., Biotechnol Bioeng 112(5), 2015
PMID: 25450749
Microarray profiling of preselected CHO host cell subclones identifies gene expression patterns associated with increased production capacity.
Harreither E, Hackl M, Pichler J, Shridhar S, Auer N, Łabaj PP, Scheideler M, Karbiener M, Grillari J, Kreil DP, Borth N., Biotechnol J 10(10), 2015
PMID: 26315449
Identification of active elementary flux modes in mitochondria using selectively permeabilized CHO cells.
Nicolae A, Wahrheit J, Nonnenmacher Y, Weyler C, Heinzle E., Metab Eng 32(), 2015
PMID: 26417715
Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cells.
Wippermann A, Klausing S, Rupp O, Albaum SP, Büntemeyer H, Noll T, Hoffrogge R., Appl Microbiol Biotechnol 98(2), 2014
PMID: 24146078
The role of replicates for error mitigation in next-generation sequencing.
Robasky K, Lewis NE, Church GM., Nat Rev Genet 15(1), 2014
PMID: 24322726
Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines.
Rupp O, Becker J, Brinkrolf K, Timmermann C, Borth N, Pühler A, Noll T, Goesmann A., PLoS One 9(1), 2014
PMID: 24427317
Analysis of microRNA transcription and post-transcriptional processing by Dicer in the context of CHO cell proliferation.
Hackl M, Jadhav V, Klanert G, Karbiener M, Scheideler M, Grillari J, Borth N., J Biotechnol 190(), 2014
PMID: 24486028
Transient receptor potential ankyrin 1 receptor activation in vitro and in vivo by pro-tussive agents: GRC 17536 as a promising anti-tussive therapeutic.
Mukhopadhyay I, Kulkarni A, Aranake S, Karnik P, Shetty M, Thorat S, Ghosh I, Wale D, Bhosale V, Khairatkar-Joshi N., PLoS One 9(5), 2014
PMID: 24819048
Multiplex real-time PCR assays for detection of four seedborne spinach pathogens.
Feng C, Mansouri S, Bluhm BH, du Toit LJ, Correll JC., J Appl Microbiol 117(2), 2014
PMID: 24823269
Advancing biopharmaceutical process science through transcriptome analysis.
Vishwanathan N, Le H, Le T, Hu WS., Curr Opin Biotechnol 30(), 2014
PMID: 25014889
CHOPPI: a web tool for the analysis of immunogenicity risk from host cell proteins in CHO-based protein production.
Bailey-Kellogg C, Gutiérrez AH, Moise L, Terry F, Martin WD, De Groot AS., Biotechnol Bioeng 111(11), 2014
PMID: 24888712
Transcriptome analysis of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 applying high-throughput sequencing of expressed sequence tags (ESTs).
Wibberg D, Jelonek L, Rupp O, Kröber M, Goesmann A, Grosch R, Pühler A, Schlüter A., Fungal Biol 118(9-10), 2014
PMID: 25209639
Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing.
Jakobi T, Brinkrolf K, Tauch A, Noll T, Stoye J, Pühler A, Goesmann A., J Biotechnol 190(), 2014
PMID: 25086342
MicroRNAs differentially present in the plasma of HIV elite controllers reduce HIV infection in vitro.
Reynoso R, Laufer N, Hackl M, Skalicky S, Monteforte R, Turk G, Carobene M, Quarleri J, Cahn P, Werner R, Stoiber H, Grillari-Voglauer R, Grillari J, Grillari J., Sci Rep 4(), 2014
PMID: 25081906
Cross-species transcriptomic approach reveals genes in hamster implantation sites.
Lei W, Herington J, Galindo CL, Ding T, Brown N, Reese J, Paria BC., Reproduction 148(6), 2014
PMID: 25252651
Hypoxia influences protein transport and epigenetic repression of CHO cell cultures in shake flasks.
Qian Y, Xing Z, Lee S, Mackin NA, He A, Kayne PS, He Q, Qian NX, Li ZJ., Biotechnol J 9(11), 2014
PMID: 25271019
Genetic and metabolomic analysis of AdeD and AdeI mutants of de novo purine biosynthesis: cellular models of de novo purine biosynthesis deficiency disorders.
Duval N, Luhrs K, Wilkinson TG, Baresova V, Skopova V, Kmoch S, Vacano GN, Zikanova M, Patterson D., Mol Genet Metab 108(3), 2013
PMID: 23394948
The emerging CHO systems biology era: harnessing the 'omics revolution for biotechnology.
Kildegaard HF, Baycin-Hizal D, Lewis NE, Betenbaugh MJ., Curr Opin Biotechnol 24(6), 2013
PMID: 23523260
Translatome analysis of CHO cells to identify key growth genes.
Courtes FC, Lin J, Lim HL, Ng SW, Wong NS, Koh G, Vardy L, Yap MG, Loo B, Lee DY., J Biotechnol 167(3), 2013
PMID: 23876478
Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome.
Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C, Xie M, Chen W, Li N, Baycin-Hizal D, Latif H, Forster J, Betenbaugh MJ, Famili I, Xu X, Wang J, Wang J, Palsson BO., Nat Biotechnol 31(8), 2013
PMID: 23873082
CHO microRNA engineering is growing up: recent successes and future challenges.
Jadhav V, Hackl M, Druz A, Shridhar S, Chung CY, Heffner KM, Kreil DP, Betenbaugh M, Shiloach J, Barron N, Grillari J, Borth N., Biotechnol Adv 31(8), 2013
PMID: 23916872
Breaking limitations of complex culture media: functional non-viral miRNA delivery into pharmaceutical production cell lines.
Fischer S, Wagner A, Kos A, Aschrafi A, Handrick R, Hannemann J, Otte K., J Biotechnol 168(4), 2013
PMID: 23994267
Chinese hamster genome database: an online resource for the CHO community at www.CHOgenome.org.
Hammond S, Kaplarevic M, Borth N, Betenbaugh MJ, Lee KH., Biotechnol Bioeng 109(6), 2012
PMID: 22105744
Computational identification of microRNA gene loci and precursor microRNA sequences in CHO cell lines.
Hackl M, Jadhav V, Jakobi T, Rupp O, Brinkrolf K, Goesmann A, Pühler A, Noll T, Borth N, Grillari J., J Biotechnol 158(3), 2012
PMID: 22306111
Utilization and evaluation of CHO-specific sequence databases for mass spectrometry based proteomics.
Meleady P, Hoffrogge R, Henry M, Rupp O, Bort JH, Clarke C, Brinkrolf K, Kelly S, Müller B, Doolan P, Hackl M, Beckmann TF, Noll T, Grillari J, Barron N, Pühler A, Clynes M, Borth N., Biotechnol Bioeng 109(6), 2012
PMID: 22389098
A screening method to assess biological effects of microRNA overexpression in Chinese hamster ovary cells.
Jadhav V, Hackl M, Bort JA, Wieser M, Harreither E, Kunert R, Borth N, Grillari J., Biotechnol Bioeng 109(6), 2012
PMID: 22407745
miRNAs--pathway engineering of CHO cell factories that avoids translational burdening.
Hackl M, Borth N, Grillari J., Trends Biotechnol 30(8), 2012
PMID: 22673691
Of [Hamsters] and men: a new perspective on host cell proteins.
Gutiérrez AH, Moise L, De Groot AS., Hum Vaccin Immunother 8(9), 2012
PMID: 23124469
How can measurement, monitoring, modeling and control advance cell culture in industrial biotechnology?
Carrondo MJ, Alves PM, Carinhas N, Glassey J, Hesse F, Merten OW, Micheletti M, Noll T, Oliveira R, Reichl U, Staby A, Teixeira AP, Weichert H, Mandenius CF., Biotechnol J 7(12), 2012
PMID: 22949408


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