Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering

Hackl M, Jakobi T, Blom J, Doppmeier D, Brinkrolf K, Szczepanowski R, Bernhart SH, Höner zu Siederdissen C, Bort JAH, Wieser M, Kunert R, et al. (2011)
Journal of Biotechnology 153(1-2): 62-75.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
DOI
Autor*in
Hackl, Matthias; Jakobi, Tobias; Blom, JochenUniBi; Doppmeier, DanielUniBi; Brinkrolf, KarinaUniBi; Szczepanowski, RafaelUniBi; Bernhart, Stephan H; Höner zu Siederdissen, Christian; Bort, Juan A Hernandez; Wieser, Matthias; Kunert, Renate; Jeffs, Simon
Alle
Einrichtung
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Institut für Bioinformatik
Abstract / Bemerkung
Chinese hamster ovary (CHO) cells are the predominant cell factory for the production of recombinant therapeutic proteins. Nevertheless, the lack in publicly available sequence information is severely limiting advances in CHO cell biology, including the exploration of microRNAs (miRNA) as tools for CHO cell characterization and engineering. In an effort to identify and annotate both conserved and novel CHO miRNAs in the absence of a Chinese hamster genome, we deep-sequenced small RNA fractions of 6 biotechnologically relevant cell lines and mapped the resulting reads to an artificial reference sequence consisting of all known miRNA hairpins. Read alignment patterns and read count ratios of 5' and 3' mature miRNAs were obtained and used for an independent classification into miR/miR* and 5p/3p miRNA pairs and discrimination of miRNAs from other non-coding RNAs, resulting in the annotation of 387 mature CHO miRNAs. The quantitative content of next-generation sequencing data was analyzed and confirmed using qPCR, to find that miRNAs are markers of cell status. Finally, cDNA sequencing of 26 validated targets of miR-17-92 suggests conserved functions for miRNAs in CHO cells, which together with the now publicly available sequence information sets the stage for developing novel RNAi tools for CHO cell engineering.
Erscheinungsjahr
2011
Zeitschriftentitel
Journal of Biotechnology
Band
153
Ausgabe
1-2
Seite(n)
62-75
ISSN
0168-1656
Page URI
https://pub.uni-bielefeld.de/record/2087955

Zitieren

Hackl M, Jakobi T, Blom J, et al. Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of Biotechnology. 2011;153(1-2):62-75.
Hackl, M., Jakobi, T., Blom, J., Doppmeier, D., Brinkrolf, K., Szczepanowski, R., Bernhart, S. H., et al. (2011). Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of Biotechnology, 153(1-2), 62-75. https://doi.org/10.1016/j.jbiotec.2011.02.011
Hackl, Matthias, Jakobi, Tobias, Blom, Jochen, Doppmeier, Daniel, Brinkrolf, Karina, Szczepanowski, Rafael, Bernhart, Stephan H, et al. 2011. “Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering”. Journal of Biotechnology 153 (1-2): 62-75.
Hackl, M., Jakobi, T., Blom, J., Doppmeier, D., Brinkrolf, K., Szczepanowski, R., Bernhart, S. H., Höner zu Siederdissen, C., Bort, J. A. H., Wieser, M., et al. (2011). Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of Biotechnology 153, 62-75.
Hackl, M., et al., 2011. Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of Biotechnology, 153(1-2), p 62-75.
M. Hackl, et al., “Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering”, Journal of Biotechnology, vol. 153, 2011, pp. 62-75.
Hackl, M., Jakobi, T., Blom, J., Doppmeier, D., Brinkrolf, K., Szczepanowski, R., Bernhart, S.H., Höner zu Siederdissen, C., Bort, J.A.H., Wieser, M., Kunert, R., Jeffs, S., Hofacker, I.L., Goesmann, A., Pühler, A., Borth, N., Grillari, J.: Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of Biotechnology. 153, 62-75 (2011).
Hackl, Matthias, Jakobi, Tobias, Blom, Jochen, Doppmeier, Daniel, Brinkrolf, Karina, Szczepanowski, Rafael, Bernhart, Stephan H, Höner zu Siederdissen, Christian, Bort, Juan A Hernandez, Wieser, Matthias, Kunert, Renate, Jeffs, Simon, Hofacker, Ivo L., Goesmann, Alexander, Pühler, Alfred, Borth, Nicole, and Grillari, Johannes. “Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering”. Journal of Biotechnology 153.1-2 (2011): 62-75.

50 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
Methods for Using Small Non-Coding RNAs to Improve Recombinant Protein Expression in Mammalian Cells.
Inwood S, Betenbaugh MJ, Shiloach J., Genes (Basel) 9(1), 2018
PMID: 29315258
Application of microRNA Targeted 3'UTRs to Repress DHFR Selection Marker Expression for Development of Recombinant Antibody Expressing CHO Cell Pools.
Jossé L, Zhang L, Smales CM., Biotechnol J 13(10), 2018
PMID: 29981248
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
Regulation of miR-29b-1/a transcription and identification of target mRNAs in CHO-K1 cells.
Muluhngwi P, Richardson K, Napier J, Rouchka EC, Mott JL, Klinge CM., Mol Cell Endocrinol 444(), 2017
PMID: 28137615
miRNA engineering of CHO cells facilitates production of difficult-to-express proteins and increases success in cell line development.
Fischer S, Marquart KF, Pieper LA, Fieder J, Gamer M, Gorr I, Schulz P, Bradl H., Biotechnol Bioeng 114(7), 2017
PMID: 28262952
Therapeutic glycoprotein production in mammalian cells.
Lalonde ME, Durocher Y., J Biotechnol 251(), 2017
PMID: 28465209
Expression Profile of microRNAs and Their Targeted Pathways in Human Ovaries Detected by Next-Generation Small RNA Sequencing.
Xu B, Zhang YW, Zheng SX, Tong XH, Liu YS., DNA Cell Biol 35(5), 2016
PMID: 26828676
A signature of 12 microRNAs is robustly associated with growth rate in a variety of CHO cell lines.
Klanert G, Jadhav V, Shanmukam V, Diendorfer A, Karbiener M, Scheideler M, Bort JH, Grillari J, Hackl M, Borth N., J Biotechnol 235(), 2016
PMID: 26993211
MicroRNAs in the Host Response to Viral Infections of Veterinary Importance.
Samir M, Vaas LA, Pessler F., Front Vet Sci 3(), 2016
PMID: 27800484
Identification and characterization of microRNAs expressed in the African malaria vector Anopheles funestus life stages using high throughput sequencing.
Allam M, Spillings BL, Abdalla H, Mapiye D, Koekemoer LL, Christoffels A., Malar J 15(1), 2016
PMID: 27825380
Sequencing technologies for animal cell culture research.
Kremkow BG, Lee KH., Biotechnol Lett 37(1), 2015
PMID: 25214225
Conserved microRNA function as a basis for Chinese hamster ovary cell engineering.
Kelly PS, Gallagher C, Clynes M, Barron N., Biotechnol Lett 37(4), 2015
PMID: 25527440
Unveiling the principle of microRNA-mediated redundancy in cellular pathway regulation.
Fischer S, Handrick R, Aschrafi A, Otte K., RNA Biol 12(3), 2015
PMID: 25826657
Annotation of additional evolutionary conserved microRNAs in CHO cells from updated genomic data.
Diendorfer AB, Hackl M, Klanert G, Jadhav V, Reithofer M, Stiefel F, Hesse F, Grillari J, Borth N., Biotechnol Bioeng 112(7), 2015
PMID: 25689160
Identification and profiling of microRNAs in goat endometrium during embryo implantation.
Song Y, An X, Zhang L, Fu M, Peng J, Han P, Hou J, Zhou Z, Cao B., PLoS One 10(4), 2015
PMID: 25886011
Towards next generation CHO cell biology: Bioinformatics methods for RNA-Seq-based expression profiling.
Monger C, Kelly PS, Gallagher C, Clynes M, Barron N, Clarke C., Biotechnol J 10(7), 2015
PMID: 26058739
Re-programming CHO cell metabolism using miR-23 tips the balance towards a highly productive phenotype.
Kelly PS, Breen L, Gallagher C, Kelly S, Henry M, Lao NT, Meleady P, O'Gorman D, Clynes M, Barron N., Biotechnol J 10(7), 2015
PMID: 26097147
miR-2861 as novel HDAC5 inhibitor in CHO cells enhances productivity while maintaining product quality.
Fischer S, Paul AJ, Wagner A, Mathias S, Geiss M, Schandock F, Domnowski M, Zimmermann J, Handrick R, Hesse F, Otte K., Biotechnol Bioeng 112(10), 2015
PMID: 25997799
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
Identification and characterization of microRNAs in pearl oyster Pinctada martensii by Solexa deep sequencing.
Jiao Y, Zheng Z, Du X, Wang Q, Huang R, Deng Y, Shi S, Zhao X., Mar Biotechnol (NY) 16(1), 2014
PMID: 23877619
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
Stable overexpression of miR-17 enhances recombinant protein production of CHO cells.
Jadhav V, Hackl M, Klanert G, Hernandez Bort JA, Kunert R, Grillari J, Borth N., J Biotechnol 175(), 2014
PMID: 24518263
Overexpression of microRNAs enhances recombinant protein production in Chinese hamster ovary cells.
Loh WP, Loo B, Zhou L, Zhang P, Lee DY, Yang Y, Lam KP., Biotechnol J 9(9), 2014
PMID: 24819042
Advancing biopharmaceutical process science through transcriptome analysis.
Vishwanathan N, Le H, Le T, Hu WS., Curr Opin Biotechnol 30(), 2014
PMID: 25014889
Identification of microRNAs specific for high producer CHO cell lines using steady-state cultivation.
Maccani A, Hackl M, Leitner C, Steinfellner W, Graf AB, Tatto NE, Karbiener M, Scheideler M, Grillari J, Mattanovich D, Kunert R, Borth N, Grabherr R, Ernst W., Appl Microbiol Biotechnol 98(17), 2014
PMID: 25052466
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
A functional high-content miRNA screen identifies miR-30 family to boost recombinant protein production in CHO cells.
Fischer S, Buck T, Wagner A, Ehrhart C, Giancaterino J, Mang S, Schad M, Mathias S, Aschrafi A, Handrick R, Otte K., Biotechnol J 9(10), 2014
PMID: 25061012
High-resolution detection of DNA binding sites of the global transcriptional regulator GlxR in Corynebacterium glutamicum.
Jungwirth B, Sala C, Kohl TA, Uplekar S, Baumbach J, Cole ST, Pühler A, Tauch A., Microbiology 159(pt 1), 2013
PMID: 23103979
An 'omics approach towards CHO cell engineering.
Datta P, Linhardt RJ, Sharfstein ST., Biotechnol Bioeng 110(5), 2013
PMID: 23322664
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
Advances in Mammalian cell line development technologies for recombinant protein production.
Lai T, Yang Y, Ng SK., Pharmaceuticals (Basel) 6(5), 2013
PMID: 24276168
Prediction of transcribed PIWI-interacting RNAs from CHO RNAseq data.
Gerstl MP, Hackl M, Graf AB, Borth N, Grillari J., J Biotechnol 166(1-2), 2013
PMID: 23639388
Transcriptomic analysis of clonal growth rate variation during CHO cell line development.
Doolan P, Clarke C, Kinsella P, Breen L, Meleady P, Leonard M, Zhang L, Clynes M, Aherne ST, Barron N., J Biotechnol 166(3), 2013
PMID: 23651948
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
Stable microRNA expression enhances therapeutic antibody productivity of Chinese hamster ovary cells.
Strotbek M, Florin L, Koenitzer J, Tolstrup A, Kaufmann H, Hausser A, Olayioye MA., Metab Eng 20(), 2013
PMID: 24144501
Dynamic mRNA and miRNA profiling of CHO-K1 suspension cell cultures.
Hernández Bort JA, Hackl M, Höflmayer H, Jadhav V, Harreither E, Kumar N, Ernst W, Grillari J, Borth N., Biotechnol J 7(4), 2012
PMID: 21751394
Genomics in mammalian cell culture bioprocessing.
Wuest DM, Harcum SW, Lee KH., Biotechnol Adv 30(3), 2012
PMID: 22079893
Construction of BAC-based physical map and analysis of chromosome rearrangement in Chinese hamster ovary cell lines.
Cao Y, Kimura S, Itoi T, Honda K, Ohtake H, Omasa T., Biotechnol Bioeng 109(6), 2012
PMID: 22012683
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
Current trends in miRNAs and their relationship with oral squamous cell carcinoma.
Pérez-Sayáns M, Pilar GD, Barros-Angueira F, Suárez-Peñaranda JM, Fernández AC, Gándara-Rey JM, García-García A., J Oral Pathol Med 41(6), 2012
PMID: 22188431
Profiling conserved microRNA expression in recombinant CHO cell lines using Illumina sequencing.
Hammond S, Swanberg JC, Polson SW, Lee KH., Biotechnol Bioeng 109(6), 2012
PMID: 22189905
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
Computational approaches to discovering noncoding RNA.
Krzyzanowski PM, Muro EM, Andrade-Navarro MA., Wiley Interdiscip Rev RNA 3(4), 2012
PMID: 22555938
miRNAs--pathway engineering of CHO cell factories that avoids translational burdening.
Hackl M, Borth N, Grillari J., Trends Biotechnol 30(8), 2012
PMID: 22673691
Identification and profiling of novel microRNAs in the Brassica rapa genome based on small RNA deep sequencing.
Kim B, Yu HJ, Park SG, Shin JY, Oh M, Kim N, Mun JH., BMC Plant Biol 12(), 2012
PMID: 23163954
Integrated miRNA, mRNA and protein expression analysis reveals the role of post-transcriptional regulation in controlling CHO cell growth rate.
Clarke C, Henry M, Doolan P, Kelly S, Aherne S, Sanchez N, Kelly P, Kinsella P, Breen L, Madden SF, Zhang L, Leonard M, Clynes M, Meleady P, Barron N., BMC Genomics 13(), 2012
PMID: 23170974

61 References

Daten bereitgestellt von Europe PubMed Central.

A uniform system for microRNA annotation.
Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T., RNA 9(3), 2003
PMID: 12592000
The role of Bcl-2 and its combined effect with p21CIP1 in adaptation of CHO cells to suspension and protein-free culture.
Astley K, Al-Rubeai M., Appl. Microbiol. Biotechnol. 78(3), 2008
PMID: 18189137
The impact of microRNAs on protein output.
Baek D, Villen J, Shin C, Camargo FD, Gygi SP, Bartel DP., Nature 455(7209), 2008
PMID: 18668037
MicroRNAs: tiny targets for engineering CHO cell phenotypes?
Barron N., Sanchez N., Kelly P., Clynes M.., 2010
MicroRNAs: target recognition and regulatory functions.
Bartel DP., Cell 136(2), 2009
PMID: 19167326
Approaches to microRNA discovery.
Berezikov E, Cuppen E, Plasterk RH., Nat. Genet. 38 Suppl(), 2006
PMID: 16736019

AUTHOR UNKNOWN, 0
MicroRNAs and cell cycle regulation.
Carleton M, Cleary MA, Linsley PS., Cell Cycle 6(17), 2007
PMID: 17786041
Origins and Mechanisms of miRNAs and siRNAs.
Carthew RW, Sontheimer EJ., Cell 136(4), 2009
PMID: 19239886
Mammalian microRNAs: experimental evaluation of novel and previously annotated genes.
Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel DP., Genes Dev. 24(10), 2010
PMID: 20413612
Molecular profiling uncovers a p53-associated role for microRNA-31 in inhibiting the proliferation of serous ovarian carcinomas and other cancers.
Creighton CJ, Fountain MD, Yu Z, Nagaraja AK, Zhu H, Khan M, Olokpa E, Zariff A, Gunaratne PH, Matzuk MM, Anderson ML., Cancer Res. 70(5), 2010
PMID: 20179198
miR-221/222 suppression protects against endoplasmic reticulum stress-induced apoptosis via p27(Kip1)- and MEK/ERK-mediated cell cycle regulation.
Dai R, Li J, Liu Y, Yan D, Chen S, Duan C, Liu X, He T, Li H., Biol. Chem. 391(7), 2010
PMID: 20624000
Microarray and proteomics expression profiling identifies several candidates, including the valosin-containing protein (VCP), involved in regulating high cellular growth rate in production CHO cell lines.
Doolan P, Meleady P, Barron N, Henry M, Gallagher R, Gammell P, Melville M, Sinacore M, McCarthy K, Leonard M, Charlebois T, Clynes M., Biotechnol. Bioeng. 106(1), 2010
PMID: 20091739
Discovering microRNAs from deep sequencing data using miRDeep.
Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N., Nat. Biotechnol. 26(4), 2008
PMID: 18392026
Most mammalian mRNAs are conserved targets of microRNAs.
Friedman RC, Farh KK, Burge CB, Bartel DP., Genome Res. 19(1), 2008
PMID: 18955434
Initial identification of low temperature and culture stage induction of miRNA expression in suspension CHO-K1 cells.
Gammell P, Barron N, Kumar N, Clynes M., J. Biotechnol. 130(3), 2007
PMID: 17570552
c-Myc suppression of miR-23a/b enhances mitochondrial glutaminase expression and glutamine metabolism.
Gao P, Tchernyshyov I, Chang TC, Lee YS, Kita K, Ochi T, Zeller KI, De Marzo AM, Van Eyk JE, Mendell JT, Dang CV., Nature 458(7239), 2009
PMID: 19219026
Rfam: updates to the RNA families database.
Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18953034
A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach.
Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML., Genome Res. 18(6), 2008
PMID: 18469162
miRBase: microRNA sequences, targets and gene nomenclature.
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381832
miRBase: tools for microRNA genomics
Griffiths-Jones S., Saini H.K., Van S., Enright A.J.., 2008
miR-17-92 cluster: ups and downs in cancer and aging.
Grillari J, Hackl M, Grillari-Voglauer R., Biogerontology 11(4), 2010
PMID: 20437201
CHO-K1 host cells adapted to growth in glutamine-free medium by FACS-assisted evolution.
Bort JA, Stern B, Borth N., Biotechnol J 5(10), 2010
PMID: 20931603
Memory efficient folding algorithms for circular RNA secondary structures.
Hofacker IL, Stadler PF., Bioinformatics 22(10), 2006
PMID: 16452114
Fast mapping of short sequences with mismatches, insertions and deletions using index structures.
Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermuller J., PLoS Comput. Biol. 5(9), 2009
PMID: 19750212
A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA.
Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD., Science 293(5531), 2001
PMID: 11452083
Pro-tumorigenic effects of miR-31 loss in mesothelioma.
Ivanov SV, Goparaju CM, Lopez P, Zavadil J, Toren-Haritan G, Rosenwald S, Hoshen M, Chajut A, Cohen D, Pass HI., J. Biol. Chem. 285(30), 2010
PMID: 20463022
Recombinant protein therapeutics from CHO Cells – 20 years and counting
Jayapal K.P., Wlaschin K.F., Hu W.S., Yap M.G.S.., 2007
Comparative analysis of HIV-1 recombinant envelope glycoproteins from different culture systems.
Jeffs SA, Goriup S, Stacey G, Yuen CT, Holmes H., Appl. Microbiol. Biotechnol. 72(2), 2006
PMID: 16447052
Conserved MicroRNAs in Chinese hamster ovary cell lines
Johnson K.C., Jacob N.M., Nissom P.M., Hackl M., Lee L.H., Yap M., Hu W.S.., 2010
Repbase Update, a database of eukaryotic repetitive elements.
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J., Cytogenet. Genome Res. 110(1-4), 2005
PMID: 16093699
Transcriptome and proteome analysis of Chinese hamster ovary cells under low temperature and butyrate treatment.
Kantardjieff A, Jacob NM, Yee JC, Epstein E, Kok YJ, Philp R, Betenbaugh M, Hu WS., J. Biotechnol. 145(2), 2009
PMID: 19770009
Developing genomic platforms for Chinese hamster ovary cells.
Kantardjieff A, Nissom PM, Chuah SH, Yusufi F, Jacob NM, Mulukutla BC, Yap M, Hu WS., Biotechnol. Adv. 27(6), 2009
PMID: 19470403
MicroRNAs and cellular phenotypy.
Kosik KS., Cell 143(1), 2010
PMID: 20887887
miRBase: integrating microRNA annotation and deep-sequencing data
Kozomara A., Griffiths-Jones S.., 2010
Methods in mammalian cell line engineering: from random mutagenesis to sequence-specific approaches.
Kramer O, Klausing S, Noll T., Appl. Microbiol. Biotechnol. 88(2), 2010
PMID: 20689950
miR-21: a small multi-faceted RNA.
Krichevsky AM, Gabriely G., J. Cell. Mol. Med. 13(1), 2009
PMID: 19175699
In-depth characterization of the microRNA transcriptome in a leukemia progression model.
Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, Heuser M, Yung E, Piper J, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst M, Hansen CL, Marra MA, Humphries RK., Genome Res. 18(11), 2008
PMID: 18849523
Evidence for human microRNA-offset RNAs in small RNA sequencing data.
Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovich P, Stadler PF., Bioinformatics 25(18), 2009
PMID: 19584066
Identification and classification of small RNAs in transcriptome sequence data
Langenberger D., Bermudez-Santana C.I., Stadler P.F., Hoffmann S., Langenberger D., Bermudez-Santana C., Hertel J., Hoffmann S., Khaitovich P., Stadler P.F.., 2009
Protein-free transfection of CHO host cells with an IgG-fusion protein: selection and characterization of stable high producers and comparison to conventionally transfected clones.
Lattenmayer C, Loeschel M, Schriebl K, Steinfellner W, Sterovsky T, Trummer E, Vorauer-Uhl K, Muller D, Katinger H, Kunert R., Biotechnol. Bioeng. 96(6), 2007
PMID: 17004273
The nuclear RNase III Drosha initiates microRNA processing.
Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, Kim VN., Nature 425(6956), 2003
PMID: 14508493
Related effects of cell adaptation to serum-free conditions on murine EPO production and glycosylation by CHO cells.
Lefloch F, Tessier B, Chenuet S, Guillaume JM, Cans P, Goergen JL, Marc A., Cytotechnology 52(1), 2006
PMID: 19002864
Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.
Livak KJ, Schmittgen TD., Methods 25(4), 2001
PMID: 11846609
Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells.
Mayr C, Bartel DP., Cell 138(4), 2009
PMID: 19703394
Applications of next-generation sequencing technologies in functional genomics.
Morozova O, Marra MA., Genomics 92(5), 2008
PMID: 18703132
MicroRNAs as targets for engineering of CHO cell factories.
Muller D, Katinger H, Grillari J., Trends Biotechnol. 26(7), 2008
PMID: 18471912
RNAdb 2.0--an expanded database of mammalian non-coding RNAs.
Pang KC, Stephen S, Dinger ME, Engstrom PG, Lenhard B, Mattick JS., Nucleic Acids Res. 35(Database issue), 2006
PMID: 17145715
The UCSC Genome Browser database: update 2010.
Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19906737
Temperature: a simple parameter for process optimization in fed-batch cultures of recombinant Chinese hamster ovary cells
Rössler B., Lübben H., Kretzmer G.., 1996
Widespread changes in protein synthesis induced by microRNAs.
Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N., Nature 455(7209), 2008
PMID: 18668040
Archiving next generation sequencing data.
Shumway M, Cochrane G, Sugawara H., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19965774
Genesis: cluster analysis of microarray data.
Sturn A, Quackenbush J, Trajanoski Z., Bioinformatics 18(1), 2002
PMID: 11836235
MicroRNAs as gatekeepers of apoptosis.
Subramanian S, Steer CJ., J. Cell. Physiol. 223(2), 2010
PMID: 20112282
CHO cells adapted to hypothermic growth produce high yields of recombinant beta-interferon.
Sunley K, Tharmalingam T, Butler M., Biotechnol. Prog. 24(4), 2008
PMID: 19194899
Genetics of somatic mammalian cells. II. Chromosomal constitution of cells in tissue culture.
TJIO JH, PUCK TT., J. Exp. Med. 108(2), 1958
PMID: 13563760
Process parameter shifting: Part II. Biphasic cultivation-A tool for enhancing the volumetric productivity of batch processes using Epo-Fc expressing CHO cells.
Trummer E, Fauland K, Seidinger S, Schriebl K, Lattenmayer C, Kunert R, Vorauer-Uhl K, Weik R, Borth N, Katinger H, Muller D., Biotechnol. Bioeng. 94(6), 2006
PMID: 16736532
Isolation of Chinese hamster cell mutants deficient in dihydrofolate reductase activity.
Urlaub G, Chasin LA., Proc. Natl. Acad. Sci. U.S.A. 77(7), 1980
PMID: 6933469
In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity.
van der Burgt A, Fiers MW, Nap JP, van Ham RC., BMC Genomics 10(), 2009
PMID: 19405940
Production of recombinant protein therapeutics in cultivated mammalian cells.
Wurm FM., Nat. Biotechnol. 22(11), 2004
PMID: 15529164
Serum protects protein-free competent Chinese hamster ovary cells against apoptosis induced by nutrient deprivation in batch culture.
Zanghi JA, Fussenegger M, Bailey JE., Biotechnol. Bioeng. 64(1), 1999
PMID: 10397845
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 21392545
PubMed | Europe PMC

Suchen in

Google Scholar