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.

Journal Article | Published | English

No fulltext has been uploaded

Abstract
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.
Publishing Year
ISSN
PUB-ID

Cite this

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.
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.
This data publication is cited in the following publications:
This publication cites the following data publications:

34 Citations in Europe PMC

Data provided by Europe PubMed Central.

Effect of Temperature Downshift on the Transcriptomic Responses of Chinese Hamster Ovary Cells Using Recombinant Human Tissue Plasminogen Activator Production Culture.
Bedoya-Lopez A, Estrada K, Sanchez-Flores A, Ramirez OT, Altamirano C, Segovia L, Miranda-Rios J, Trujillo-Roldan MA, Valdez-Cruz NA., PLoS ONE 11(3), 2016
PMID: 26991106
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
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, Labaj PP, Scheideler M, Karbiener M, Grillari J, Kreil DP, Borth N., Biotechnol J 10(10), 2015
PMID: 26315449
Sequencing technologies for animal cell culture research.
Kremkow BG, Lee KH., Biotechnol. Lett. 37(1), 2015
PMID: 25214225
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
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
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, Puhler A, Goesmann A., J. Biotechnol. 190(), 2014
PMID: 25086342
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
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

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 21945585
PubMed | Europe PMC

Search this title in

Google Scholar