Bioreactor - OmicsDI

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Genomics (3774)
Unknown (3462)
Transcriptomics (439)
Proteomics (99)
Metabolomics (24)
Models (8)
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Methylation profiling (2)

Organisms

Homo sapiens (93)
Saccharomyces cerevisiae (80)
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Mus musculus (16)
Aspergillus niger (13)
Yarrowia lipolytica (9)
Cricetulus griseus (7)
Clostridium acetobutylicum (6)
Escherichia coli str. K-12 substr. MG1655 (6)
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Corynebacterium glutamicum ATCC 13032 (4)
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Thermotoga maritima MSB8 (3)
Saccharopolyspora erythraea (3)
Rhodospirillum rubrum (3)
Gluconobacter oxydans 621H (3)
Penicillium chrysogenum (3)
bioreactor metagenome (3)
Porphyromonas gingivalis (3)
Bacillus subtilis (3)
Escherichia coli K-12 (3)
Methanothermobacter thermautotrophicus (2)
Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (2)
Nitrosomonas europaea ATCC 19718 (2)
Methanothermobacter marburgensis str. Marburg (1)
Methanothermobacter thermautotrophicus str. Delta H (1)

Organisms

bioreactor metagenome (2076)
bioreactor sludge metagenome (310)
wastewater metagenome (126)
Homo sapiens (73)
Saccharomyces cerevisiae (67)
activated sludge metagenome (40)
sediment metagenome (33)
sludge metagenome (33)
biofilm metagenome (18)
Heyndrickxia coagulans CSIL1 (14)
anaerobic digester metagenome (10)
Aspergillus niger (9)
compost metagenome (9)
Mus musculus (9)
Capra hircus (8)
soil metagenome (7)
Escherichia coli (6)
unidentified (4)
Pseudomonas aeruginosa PAO1 (4)
Methylotuvimicrobium buryatense (3)
Nitrosomonas europaea ATCC 19718 (3)
Yarrowia lipolytica (3)
Sus scrofa (3)
Ogataea parapolymorpha (2)
Clostridium acetobutylicum (2)
Saccharopolyspora erythraea (2)
Candidatus Kuenenia stuttgartensis (2)
Streptomyces albus (2)
Cricetulus griseus (2)
biogas fermenter metagenome (2)

Repository

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geo (133)
pride (88)
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Disease

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Technology Type

Mass Spectrometry (88)
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Instrument Platform

Illumina HiSeq 2000 (6)
NextSeq 500 (6)
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Trizol (Invitrogen); FastPrep (MP Biochemicals) (3)
DASGIP bioreactors (3)
Ion Torrent Proton (3)
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Illumina NovaSeq 6000 (3)
Illumina HiSeq 3000 (3)
Illumina HiSeq 4000 (3)
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Agilent Micro Array Scanner G2565CA (2)
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Axon- GenePix4000B (2)
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MaXis (2)
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3 L BioFlo®/CelliGen® 115 Bioreactor (New Brunswick Scientific) (1)
Applikon (1)
RiboZ (1)
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Computerome (1)
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GenePix 4000B [Axon Instruments] (1)
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Publication Date

2014 (52)
2013 (46)
2012 (43)
2024 (40)
2010 (40)
2011 (35)
2008 (35)
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2015 (33)
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2016 (28)
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2021 (25)
2009 (19)
2018 (16)
2019 (16)
2017 (11)
2007 (6)
2006 (5)
2004 (1)

CHEBI ID

CHEBI:62890 (3)
CHEBI:139151 (3)
CHEBI:85106 (3)
CHEBI:40356 (3)
CHEBI:67138 (3)
CHEBI:64076 (3)
CHEBI:64074 (3)
CHEBI:64077 (3)
CHEBI:64075 (3)
CHEBI:70731 (3)
CHEBI:13388 (3)
CHEBI:35098 (3)
CHEBI:34773 (3)
CHEBI:34606 (3)
CHEBI:74004 (3)
CHEBI:74007 (3)
CHEBI:134176 (3)
CHEBI:74853 (3)
CHEBI:71517 (3)
CHEBI:58838 (3)
CHEBI:58837 (3)
CHEBI:57677 (3)
CHEBI:60464 (3)
CHEBI:65078 (3)
CHEBI:48595 (3)
CHEBI:73682 (3)
CHEBI:27973 (3)
CHEBI:131350 (3)
CHEBI:45506 (3)
CHEBI:58556 (3)

Metabolite Name

Adenosine (5)
Mannitol (4)
Succinate (4)
Glycine (4)
L-Glutamic acid (4)
Inosine (4)
Valine (3)
Thymine (3)
6-Phosphogluconic acid (3)
Triethanolamine (3)
Indole (3)
Methionine (3)
Glyceric acid (3)
Malic acid (3)
Tyrosine (3)
Threonine (3)
Phenylalanine (3)
L-Tryptophan (3)
Uracil (3)
Hypoxanthine (3)
Adenine (3)
Guanine (3)
L-Histidine (3)
L-Arginine (3)
L-Phenylalanine (3)
L-Alanine (3)
DL-p-Hydroxyphenyllactic acid (2)
3-Phospho-D-erythronate (2)
3-Methoxy-4,5-methylenedioxycinnamaldehyde (2)
3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid (2)

IsPrivate

False (5)

Submitter Keywords

FROG (3)

First Public Date

2024 (653)
2026 (603)
2025 (380)
2017 (356)
2021 (345)
2019 (259)
2023 (182)
2020 (180)
2018 (176)
2016 (160)
2022 (140)
2014 (136)
2015 (116)
2013 (69)

Classification

bacteria (33)
fungi (10)
protozoa (1)

Modelling Approach

Constraint-based model (4)

Study type

Transcription profiling by array (247)
RNA-seq of coding RNA (39)
Other (8)
Unknown experiment type (7)
ChIP-seq (5)
High-throughput sequencing (4)
Transcription profiling by tiling array (4)
Cell line - High-throughput sequencing (3)
Genotyping by array (3)
One-color microarray (2)
RNA-seq of coding RNA from single cells (2)
RNA-seq of non coding RNA (2)
Comparative genomic hybridization by array (1)
DNA-seq (1)
RNA-seq of total RNA (1)

Release Date

2022 (400)
2025 (372)
2021 (369)
2023 (363)
2024 (326)
2020 (313)
2019 (254)
2018 (229)
2017 (177)
2016 (161)
2015 (145)
2014 (141)
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2012 (93)
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2009 (35)
2006 (11)
2007 (10)
2005 (9)
2003 (5)
2002 (4)
2001 (4)
2004 (2)
2000 (2)
1999 (1)
1998 (1)
1996 (1)

Lab affiliation

Centre of Biological Engineering, Minho University (4)
Proteomics Mass Spectrometry, University of Tasmania (2)
University of California Los Angeles (2)
Cell Culture Technology, Technical Faculty, Bielefeld University, Germany (2)
School of Chemistry and Molecular Biosciences, The University of Queensland (2)
Vanderbilt University Proteomics Core (2)
Department of Biotechnology, Delft University of Technology, The Netherlands. (2)
iBET, Instituto de Biologia Experimental e Biológica, Oeiras, Portugal Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal (2)
Bioprocessing Technology Institute , Agency for Science, Technology and Research-A*STAR, 20 Biopolis Way 06-01, Singapore 138668, Republic of Singapore (1)
Science for Life Laboratory, School of Biotechnology, KTH – Royal Institute of Technology, Stockholm, Sweden. (1)
Archaea Biology and Ecogenomics Department of Functional and Evolutionary Ecology University of Vienna (1)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (1)
Chair Plant Biotechnology Faculty of Biology University of Freiburg Schaenzlestrasse 1 D-79104 Freiburg Germany (1)
Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Germany (1)
Forschungszentrum Juelich GmbH Institute of Bio- and Geosciences 1 Systems Biotechnology Group: Quantitative Microbial Phenotyping (1)
Helmholtz Centre for Environmental Research - UFZ, Department of Molecular Systems Bioloy (1)
University of Lille (1)
Institute of Bio- and Geosciences IBG-1: Biotechnology Forschungszentrum Jülich GmbH 52425 Jülich Germany (1)
Institut fuer Mikrobiologie EMAU Greifswald (1)
Helmholtz Centre for Environmental Research GmbH - UFZ Department of Molecular Systems Biology Permoserstra��e 15, 04318 Leipzig, Germany Phone +49 341 235 4767 nico.jehmlich@ufz.de, www.ufz.de (1)
Helmholtz-Centrte for Environmental Research - UFZ GmbH Department of Molecular Systems Biology Permoserstr. 15 04318 Leipzig, Germany (1)
Proteome center Tuebingen 15 Auf der Morgenstelle 72074 Tübingen Germany (1)
University of southern Denmark Department of Biochemistry and Molecular Biology Protein Research group Denmark (1)
aDepartment of Chemistry and Bioscience, Aalborg University, Aalborg East, Denmark (1)
Director of the Wellcome Centre for Cell-Matrix Research Wellcome Trust Centre for Cell Matrix Research School of Biological Sciences Faculty of Biology, Medical and Health Sciences University of Manchester (1)
Centre Algatech, Institute of Microbiology, Academy of Sciences of the Czech Republic, Třeboň,CZ. (1)
The University of Queensland, Australia (1)
Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany (1)
University of Tübingen Center for Applied Geosciences Environmental Biotechnology Group (1)
John van Geest Cancer Research Centre, Nottingham Trent University (1)

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Harnessing a Germ-Free Mouse Gut Bioreactor for Directed Evolution of Probiotics to Combat NAFLD

The data uploaded in this study were obtained from an interventional experiment in which non-alcoholic fatty liver disease (NAFLD) model mice were treated with either the original or adapted bacterial strains, followed by fecal sample collection and targeted bile acid metabolomic analysis.

2026-01-20 | MTBLS13718 | MetaboLights

Toward industrial C8 production: Oxygen intrusion drives renewable n caprylate production from ethanol and acetate via intermediate metabolite production

Previous bioreactor studies achieved high volumetric n caprylate (i.e., n octanoate) production rates and selectivities from ethanol and acetate with chain elongating microbiomes. However, the metabolic pathways from the substrates to n caprylate synthesis were unclear. We operated two n caprylate p...

ORGANISM(S): bioreactor metagenome

2025-05-24 | PXD054148 | Pride