Systems and Synthetic Biology

Search results

• Transcriptomics datasets for Clostridium autoethanogenum grown on CO in different environmental conditions

  Diender, M. (Creator), Koehorst, J. (Creator) & Machado de Sousa, D. (Creator), Wageningen University & Research, 25 Jan 2019

  DOI: 10.4121/uuid:b6bd64a9-5bdb-4655-9829-520aa4600987

  Dataset

• Expected and observed genotype complexity in prokaryotes: correlation between 16S-rRNA phylogeny and protein domain content

  Koehorst, J. (Creator), Schaap, P. (Contributor) & Suarez Diez, M. (Contributor), Wageningen University & Research, 24 Oct 2018

  DOI: 10.4121/uuid:37346f1e-f8cf-4112-ba4b-1223a3e4edda

  Dataset

• Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data

  Koehorst, J. (Creator), van Dam, J. C. J. (Contributor), van Heck, R. G. A. (Contributor), Saccenti, E. (Contributor), Martins dos Santos, V. (Contributor), Suarez Diez, M. (Contributor) & Schaap, P. (Contributor), Wageningen University & Research, 25 Sep 2018

  DOI: 10.4121/uuid:948c10fe-7ea5-47f3-bdb2-d5b0f908820b

  Dataset

• Rhizopus delemar LC-MS/MS high low oxygen

  Odoni, D. I. (Creator) & Martins dos Santos, V. (Creator), Wageningen University, 15 Feb 2017

  https://www.ebi.ac.uk/pride/archive/projects/PXD004600

  Dataset

• In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions

  Kampers, L. F. C. (Creator), van Heck, R. G. A. (Creator), Donati, S. (Creator), Saccenti, E. (Creator), Volkers, R. J. M. (Creator), Schaap, P. (Creator), Suarez Diez, M. (Creator), Nikel, P. I. (Creator) & Martins dos Santos, V. (Creator), Wageningen University & Research, 23 Oct 2019

  DOI: 10.6084/m9.figshare.c.4708994

  Dataset

• Genome sequence of Romboutsia str. Frifi

  Gerritsen, J. (Creator), Umanetc, A. (Creator), van Leeuwen-Staneva, I. N. (Creator), Hornung, B. V. H. (Creator), Ritari, J. (Creator), Paulin, L. (Creator), Rijkers, G. T. (Creator), de Vos, W. (Creator) & Smidt, H. (Creator), Wageningen University, 17 Mar 2018

  https://www.ebi.ac.uk/ena/data/view/PRJEB7106

  Dataset

• Genome sequence of Desulfitobacterium hafniense PCE-S

  Goris, T. (Creator), Hornung, B. V. H. (Creator), Kruse, T. (Creator), Reinhold, A. (Creator), Westermann, M. (Creator), Schaap, P. (Creator), Smidt, H. (Creator) & Diekert, G. (Creator), Wageningen University, 15 Oct 2014

  https://www.ebi.ac.uk/ena/data/view/PRJEB6708

  Dataset

• Genome sequence of Romboutsia lituseburensis

  Gerritsen, J. (Creator), Umanetc, A. (Creator), van Leeuwen-Staneva, I. N. (Creator), Hornung, B. V. H. (Creator), Ritari, J. (Creator), Paulin, L. (Creator), Rijkers, G. T. (Creator), de Vos, W. (Creator) & Smidt, H. (Creator), Wageningen University, 4 Aug 2018

  https://www.ebi.ac.uk/ena/data/view/PRJEB7306

  Dataset

• The transcriptional response of bioreactor-grown Aspergillus niger cultures towards three oils

  van der Veen, D. (Creator), van den Berg, R. A. (Creator) & de Graaff, L. (Creator), Wageningen University and Research Centre, 1 Sep 2009

  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14285

  Dataset

• Determination of variability of fermentor-grown Aspergillus niger

  van der Veen, D. (Creator), Pimenta Ferreira De Oliveira, J. (Creator), van den Berg, W. (Creator) & de Graaff, L. (Creator), Wageningen University and Research Centre, 31 Dec 2008

  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11405

  Dataset

• Microbial community response of an organohalide respiring enrichment culture to permanganate oxidation

  Sutton, N. (Creator), Atashgahi, S. (Creator), Saccenti, E. (Creator), Grotenhuis, T. (Creator), Smidt, H. (Creator) & Rijnaarts, H. (Creator), Wageningen University, 29 May 2015

  https://www.ebi.ac.uk/ena/data/view/PRJEB8632

  Dataset

• Scenedesmus Obliquus UTEX393 draft genome

  Carreres, B. M. (Creator), de Jaeger, L. (Creator), Springer, J. (Creator), Barbosa, M. (Creator), Breuer, G. (Creator), van den End, F. (Creator), Kleinegris, D. M. M. (Creator), Schäffers, I. (Creator), Wolbert, E. (Creator), Zhang, H. (Creator), Lamers, P. P. (Creator), Martins dos Santos, V. (Creator), Wijffels, R. (Creator), Eggink, G. (Creator), Schaap, P. (Creator) & Martens, D. (Creator), Wageningen University, 1 Nov 2016

  https://www.ebi.ac.uk/ena/data/view/PRJEB15865

  Dataset

• Genome sequencing of one-carbon degrading acetogenic bacteria Moorella glycerini Strain NMP

  Liebensteiner, M. (Creator), Pinkse, M. W. H. (Creator), Nijsse, B. (Creator), Verhaert, P. D. E. M. (Creator), Tsesmetzis, N. (Creator), Stams, F. (Creator) & Lomans, B. (Creator), Wageningen University, 5 Feb 2015

  http://www.ebi.ac.uk/ena/data/view/PRJEB8377

  Dataset

• High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasis

  Benis, N. (Creator), Wells, J. (Creator), Smits, M. (Creator), Kar, S. (Creator), van der Hee, B. (Creator), Martins dos Santos, V. (Creator) & Schokker, D. (Creator), Wageningen University & Research, 31 Dec 2019

  DOI: 10.6084/m9.figshare.c.4801542

  Dataset

• NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes

  Ramiro Garcia, J. (Creator), Hermes, G. (Creator), Giatsis, C. (Creator), Sipkema, D. (Creator), Zoetendal, E. (Creator), Schaap, P. (Creator) & Smidt, H. (Creator), Wageningen University, 11 Nov 2015

  https://www.ebi.ac.uk/ena/data/view/PRJEB11702

  Dataset

• Organic acids production from starch waste by rumen microorganisms

  Palakawong Na Ayudthaya, S. (Creator), Hornung, B. V. H. (Creator), Ravikumar Varadarajan, A. (Creator), Plugge, W. (Creator) & Plugge, C. (Creator), Wageningen University, 21 Dec 2016

  https://www.ebi.ac.uk/ena/data/view/PRJEB6322

  Dataset

• The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows

  Vaidya, J. D. (Creator), van den Bogert, B. (Creator), Edwards, J. (Creator), Boekhorst, J. (Creator), van Gastelen, S. (Creator), Saccenti, E. (Creator), Plugge, C. (Creator) & Smidt, H. (Creator), Wageningen University, 17 Oct 2017

  https://www.ebi.ac.uk/ena/data/view/PRJEB22996

  Dataset

• Comparative genomic and physiological analysis of Trichococcus species

  Strepis, N. (Creator), Naranjo, H. D. (Creator), Meier-Kolthoff, J. P. (Creator), Göker, M. (Creator), Shapiro, N. (Creator), Kyrpides, N. C. (Creator), Klenk, H. P. (Creator), Schaap, P. (Creator), Stams, F. (Creator) & Machado de Sousa, D. (Creator), Wageningen University, 11 Apr 2016

  https://www.ncbi.nlm.nih.gov/bioproject/PRJEB12706/

  Dataset

• RNA-targeting by the Type III-A CRISPR-Cas complex of Thermus thermophilus

  Staals, R. (Creator), Zhu, Y. (Creator), Taylor, D. W. (Creator), Kornfeld, J. E. (Creator), Sharma, K. (Creator), Barendregt, A. (Creator), Koehorst, J. (Creator), Vlot, M. (Creator), Neupane, N. (Creator), Varossieau, K. (Creator), Sakamoto, K. (Creator), Suzuki, T. (Creator), Schaap, P. (Creator), Urlaub, H. (Creator), Heck, A. J. R. (Creator), Nogales, E. (Creator), Doudna, J. A. (Creator), Shinkai, A. (Creator) & van der Oost, J. (Creator), Wageningen University, 9 Oct 2014

  http://www.ebi.ac.uk/ena/data/view/PRJEB7461

  Dataset

• Comparative genomic and physiological analysis of Trichococcus species

  Strepis, N. (Creator), Sanchez Andrea, I. (Creator), van Gelder, T. (Creator), van Kruistum, H. (Creator), Shapiro, N. (Creator), Kyrpides, N. (Creator), Göker, M. (Creator), Klenk, H. P. (Creator), Schaap, P. (Creator), Stams, F. (Creator) & Machado de Sousa, D. (Creator), Wageningen University, 10 Apr 2016

  https://www.ebi.ac.uk/ena/data/view/PRJEB12707

  Dataset

• Comparative genomics, symbiotic capacities and high metabolic flexibility of the marine genus Pseudovibrio

  Versluis, D. (Creator), Nijsse, B. (Creator), Mohamad, M. A. N. (Creator), Koehorst, J. (Creator), Wiese, J. (Creator), Imhoff, J. F. (Creator), Schaap, P. (Creator), van Passel, M. W. J. (Creator), Smidt, H. (Creator) & Sipkema, D. (Creator), Wageningen University, 28 Jun 2017

  https://www.ebi.ac.uk/ena/data/view/PRJEB20602

  Dataset

• Diurnal dynamics of gaseous and dissolved metabolites and microbiota composition in the bovine rumen

  van Lingen, H. (Creator), Edwards, J. (Creator), Vaidya, J. D. (Creator), van Gastelen, S. (Creator), Saccenti, E. (Creator), van den Bogert, B. (Creator), Bannink, A. (Creator), Smidt, H. (Creator), Plugge, C. (Creator) & Dijkstra, J. (Creator), Wageningen University, 9 Jan 2018

  https://www.ebi.ac.uk/ena/data/view/PRJEB17837

  Dataset

• Genome sequence of organohalide-respiring Desulfoluna spongiiphila DBB and Desulfoluna butyratoxydans MSL71T

  Peng, P. (Creator), Goris, T. (Creator), Lu, Y. (Creator), Nijsse, B. (Creator), Burrichter, A. (Creator), Schleheck, D. (Creator), Koehorst, J. (Creator), Liu, J. (Creator), Sipkema, D. (Creator), Sinninghe Damste, J. S. (Creator), Stams, F. (Creator), Häggblom, M. M. (Creator), Smidt, H. (Creator) & Atashgahi, S. (Creator), Wageningen University, 15 May 2019

  https://www.ebi.ac.uk/ena/data/view/PRJEB31368

  Dataset

• CRISPR Cas3 Plasmid degradation assays

  Kunne, T. A. (Creator), Kieper, S. (Creator), Bannenberg, J. (Creator), Vogel, A. I. M. (Creator), Miellet, W. (Creator), Klein, M. (Creator), Depken, M. (Creator), Suarez Diez, M. (Creator) & Brouns, S. J. J. (Creator), Wageningen University, 16 Aug 2016

  https://www.ebi.ac.uk/ena/data/view/PRJEB13999

  Dataset

• Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol

  Atashgahi, S. (Creator), Lu, Y. (Creator), Zheng, Y. (Creator), Saccenti, E. (Creator), Suarez Diez, M. (Creator), Ramiro Garcia, J. (Creator), Eisenmann, H. (Creator), Elsner, M. (Creator), Stams, F. (Creator), Springael, D. (Creator), Dejonghe, W. (Creator) & Smidt, H. (Creator), Wageningen University & Research, 1 Sep 2016

  https://www.ebi.ac.uk/ena/browser/view/PRJEB13312

  Dataset