Submerged culture

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Transcriptomics (298)
Unknown (242)
Genomics (64)
Proteomics (36)
Metabolomics (10)

Organisms

Homo sapiens (52)
Arabidopsis thaliana (38)
Mycobacterium tuberculosis (27)
Staphylococcus aureus (23)
Mus musculus (12)
Sus scrofa (8)
Campylobacter jejuni (7)
Escherichia coli (7)
Aspergillus niger (7)
Neisseria meningitidis (6)
Salmonella enterica (5)
Streptococcus pneumoniae (5)
Clostridium acetobutylicum (4)
Rattus norvegicus (4)
Yersinia enterocolitica (3)
Mycobacterium tuberculosis H37Rv (3)
Candida albicans (3)
Neurospora crassa (3)
Yersinia pseudotuberculosis (2)
Mycobacterium avium (2)
Listeria monocytogenes (2)
Bos taurus (2)
Escherichia coli K-12 (2)
Cryptococcus neoformans (2)
Pseudomonas aeruginosa (2)
Meloidogyne chitwoodi (1)
Piloderma croceum (1)
Serendipita vermifera (1)
Pseudomonas syringae (1)
Pyronema omphalodes (1)

Organisms

Homo sapiens (15)
Aspergillus niger (3)
Thermothelomyces thermophilus (3)
Mus musculus (3)
Fusarium fujikuroi (1)
Aspergillus fumigatus (1)
Aspergillus terreus (1)
Salmonella enterica subsp. enterica serovar Typhimurium (1)
Aspergillus nidulans (1)
Pyronema omphalodes CBS 100304 (1)
Eremothecium gossypii (1)
Iris tectorum (1)
Tuber borchii (1)
Rangifer tarandus (1)
Podospora anserina (1)
Shiraia bambusicola (1)
Amphimedon queenslandica (1)
Brassica napus (1)
Bacillus subtilis (1)
Sus scrofa (1)
Rattus norvegicus (1)
Arabidopsis thaliana (1)
Neurospora crassa (1)

Repository

biostudies-arrayexpress (282)
ENA (59)
pride (34)
geo (20)
MetaboLights (10)
EGA (2)
iProX (1)

Tissue

Cell culture (8)
Permanent cell line cell (3)
Culture fluid (2)
Cell suspension culture (2)
Photosynthetic cell (2)
Epithelial cell (2)
Bronchial epithelial cell line (1)
Culture condition:beech wood-grown cell (1)
Culture supernatant (1)
Fungal cell (1)
Mycelium (1)
Embryonic fibroblast (1)
Mesenchymal cell (1)
Plant cell (1)
Root (1)
Whole body (1)
Leaf (1)
Lung (1)

Disease

Disease free (3)
Normal (2)
Primary tumor (1)
Oligodendroglioma (1)
Dukes D primary colon cancer (1)
Giant cell glioblastoma (1)
Colon cancer metastasis (1)
Benign adenoma (1)
Lung cancer (1)
Fibrosarcoma (1)
Parkinson's disease (1)
Giardiasis (1)
COVID-19 (1)

Technology Type

Mass Spectrometry (34)
Shotgun proteomics (16)
Mass spectrometry (9)
Bottom-up proteomics (9)
Data-dependent acquisition (6)
Gel-based experiment (5)
Data-independent acquisition (4)
Mass spectrometry assay (1)
SWATH MS (1)
Affinity purification coupled with mass spectrometry proteomics (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)

Instrument Platform

Variable Atmosphere Incubator (8)
Spectronic Helios Alpha UV-Vis spectrophotometer (7)
Bioanalyser (7)
NanoDrop (6)
Illumina NovaSeq 6000 (6)
Ultracentrifuge (4)
GeneQuant (3)
Chemostat (3)
NextSeq 550 (3)
Illumina HiSeq 2500 (3)
Illumina HiSeq 4000 (3)
Ultrospec 3000 (2)
Anaerobic workstation with airlock (2)
Nanodrop N1000 spectrophotometer (2)
ScanArray 5000 [PerkinElmer] (2)
BD GasPak 150 Jar (2)
GenePix 4000A [Axon Instruments] (2)
Jencons Millennium CO2 Incubator (2)
Axon- GenePix4000B (2)
Bellco roll-in incubator (2)
Illumina HiSeq 2000 (2)
Chromium Next GEM Chip G (1)
Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis. (1)
Lightwave (1)
Agilent G2565BA scanner (1)
Agilent Hybridization Oven (1)
Axon GenePix 4000A scanning hardware (1)
Biotech Photometer (1)
Affymetrix 428 (1)
Agilent Hybridization Oven. (1)

Publication Date

2010 (37)
2009 (37)
2008 (30)
2012 (27)
2011 (26)
2007 (26)
2013 (22)
2015 (19)
2025 (14)
2024 (13)
2022 (13)
2014 (12)
2026 (11)
2016 (11)
2023 (9)
2005 (9)
2006 (8)
2018 (6)
2017 (5)
2020 (3)
2004 (2)
2019 (2)
2021 (2)
2003 (1)

CHEBI ID

CHEBI:30769 (4)
CHEBI:6650 (3)
CHEBI:22660 (3)
CHEBI:17351 (3)
CHEBI:15713 (2)
CHEBI:17553 (2)
CHEBI:16831 (2)
CHEBI:16010 (2)
CHEBI:25017 (2)
CHEBI:18186 (2)
CHEBI:30915 (2)
CHEBI:18292 (2)
CHEBI:17659 (2)
CHEBI:28044 (2)
CHEBI:18237 (2)
CHEBI:17566 (2)
CHEBI:72998 (2)
CHEBI:15940 (2)
CHEBI:16761 (2)
CHEBI:17154 (2)
CHEBI:16335 (2)
CHEBI:16027 (2)
CHEBI:16704 (2)
CHEBI:16750 (2)
CHEBI:27897 (2)
CHEBI:16914 (2)
CHEBI:26078 (2)
CHEBI:28842 (2)
CHEBI:15756 (2)
CHEBI:72868 (1)

Metabolite Name

Adenosine diphosphate (2)
Jasmonic acid (2)
Trihydroxy octadecenoic acid (TriHOME isomer II) (1)
Trihydroxy octadecenoic acid (TriHOME isomer I) (1)
Trihydroxy octadecadienoic acid (TriHODE isomer II) (1)
Dihydroxy eicosatetraenoic acid (DiHETE) (1)
Trihydroxy octadecadienoic acid (TriHODE isomer I) (1)
Alpha-Tomatine (1)
Acetyl tryptophan (1)
Feruloyl serotonin (1)
Indole acrylic acid (1)
Caffeoyl putrescine (1)
Skatol (1)
Simvastatin lactone (1)
Phosphatidylcholine(18:0/18:1w9) (1)
GPCho(34:0) (1)
GPCho(18:3n3/18:3n3) (1)
GPCho(18:2w6/18:2w6) (1)
N-Stearoylethanolamide (1)
12-Hydroxy-Octadecanoic Acid (1)
L-Hexanoic acid ester with (3-carboxy-2-hydroxypropyl)trimethylammonium hydroxide inner salt (1)
(Z)-N-[(E,2S,3R)-1,3-bis(oxidanyl)octadec-4-en-2-yl]docos-13-enamide (1)
(3R)-3-[(Z)-octadec-9-enoyl]oxy-4-(trimethylazaniumyl)butanoate (1)
(-)-Tetradecanoylcarnitine (1)
L-gamma-glutamyl-l-alpha-aminobutyrylglycine (1)
N-(1,5-dimethyl-3-oxidanylidene-2-phenyl-pyrazol-4-yl)methanamide (1)
C18 Sphingomyelin (1)
OSF (1)
N-L-gamma-Glutamyl-L-tyrosine (1)
2-amino-5-[(1-carboxy-2-phenyl-ethyl)amino]-5-keto-valeric acid (1)

First Public Date

2024 (15)
2022 (8)
2021 (6)
2025 (5)
2023 (4)
2015 (4)
2014 (4)
2026 (3)
2018 (3)
2017 (3)
2016 (2)
2020 (1)
2019 (1)

Classification

fungi (7)
bacteria (1)

Study type

Transcription profiling by array (242)
RNA-seq of coding RNA (14)
Comparative genomic hybridization by array (7)
Unknown experiment type (4)
RNA-seq of total RNA (4)
RNA-seq of coding RNA from single cells (3)
ChIP-chip by array (2)
Transcription profiling by SAGE (1)
Ribo-seq (1)
Other (1)
ChIP-seq (1)
MicroRNA profiling by array (1)
Proteomic profiling by array (1)

Release Date

2022 (46)
2009 (38)
2010 (37)
2023 (35)
2012 (31)
2008 (31)
2015 (28)
2011 (28)
2007 (27)
2013 (26)
2025 (24)
2021 (23)
2014 (22)
2020 (18)
2019 (18)
2017 (17)
2016 (17)
2024 (16)
2018 (15)
2005 (9)
2006 (8)
2026 (4)
2004 (2)
2003 (2)
2002 (1)
2000 (1)

Lab affiliation

Department of Orthopaedics, Peking University Third Hospital (2)
Division of Physical Chemistry, Institute Ruđer Bošković, Zagreb, Croatia (1)
Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa (1)
Department of Biochemistry & Molecular Biology Michigan State University (1)
University of Edinburgh, UK (1)
Department of Pharmaceutical Sciences, University of Illinois at Chicago (1)
Glycoproteomics Lab, Parasitology department, Institute of Biomedical Sciences of University of São Paulo, Brazil. (1)
Department of Biochemistry & Molecular Biology, Michigan State Univeristy (1)
INBIOTEC-CONICET (1)
Australian Institute of Tropical Health and Medicine. Centre for Molecular Therapeutics. James Cook Univerisity, Cairns. (1)
VIB-UGent Center for Plant Systems Biology, Belgium (1)
Department of Microgravity and Translational Regenerative Medicine, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany (1)
College of Life Science, Capital Normal University, Beijing 100048, China (1)
Department of Chemistry, University of Rochester, United States (1)
Institute for Microbial and Biochemical Sciences, Forest Products Laboratory, U.S. Department of Agriculture (1)
Lab of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium (1)
Departamento de Bioquímica Setor de Ciências Biológicas Centro Politécnico Universidade Federal do Paraná BRAZIL (1)
Industrial Biotechnology, Chalmers University of Technology (1)
Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110 Ioannina, Greece (1)
Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, Hunan, P.R. China (1)
Jiangsu Academy of Agricultural Sciences (1)
International Centre for Genetic Engineering and Biotechnology Aruna Asaf Ali Marg 110 067 New Delhi, India (1)
University of Manitoba (1)
Department of Agricultural Chemistry, Edaphology and Microbiology, Microbiology area, Severo Ochoa building (C6), Agrifood Campus of International Excellence ceiA3, University of Córdoba, Córdoba, Spain (1)
University of Washington Department of Genome Sciences (1)
Ruhr-University Bochum Medizinisches Proteom-Center Clinical Proteomics - Translational Proteomics and University Hospital Knappschaftskrankenhaus Bochum Department of Anesthesia, Intensive Care Medicine, and Pain Therapy (1)
Helmholtz Centre for Environmental Research GmbH - UFZ Department of Molecular Systems Biology Permoserstraße 15, 04318 Leipzig, Germany (1)
Associate professor Universidad Nacional de Colombia campus Bogotá Facultad de Ciencias Departamento de Química Investigation group: Actividades Metabólicas Vegetales (1)
Laboratory of Mass Spectrometry BIOCEV Faculty of Science Charles University in Prague Průmyslová 595, 252 42 Vestec, Tel +420325873925 http://www.biocev.eu/corefacilit/omics/ (1)
Molecular Biology and Genetics, Cornell University, USA (1)

Tags

pathogen (8)
pathogen:fungus (7)
pathogen:bacterium (1)

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Limitations of a submerged culture system

PRJNA834644 | ENA

Next-generation sequence analysis of the submerged Iris tectorum in plant culture and in plant-algae co-culture

PRJNA503565 | ENA

Insight into cordycepin biosynthesis of Cordyceps militaris: Comparison between a liquid surface culture and a submerged culture through transcriptomic analysis.

Not available

S-EPMC5665525 | biostudies-literature

The global transcriptional effect of exogenously added butyrolactone I on Aspergillus terreus under submerged culture

The filamentous fungus Aspergillus terreus is known to produce both industrially and pharmaceutically important secondary metabolites. The objective of this study is to investigate the effect of exogenously added butyrolactone I (BI) on the submerged culture of A. terreus, especially on the possible...

ORGANISM(S): Aspergillus terreus Aspergillus terreus NIH2624

2017-05-08 | GSE93552 | GEO

Next-generation sequence analysis of the submerged Iris tectorum in plant culture and in plant-algae co-culture

We conducted a culture experiment by deeply submerging plants in swine wastewater in culturing Iris tectorum and co-culturing Iris tectorum and Dictyosphaerium sp., and found that the plants grew sub-normal in the plant-microalgae co-culture while the plants were dead after 21 days in the plant cult...

ORGANISM(S): Iris tectorum

2018-11-03 | GSE122095 | GEO

Metabolic comparison of aerial and submerged mycelia formed in the liquid surface culture of Cordyceps militaris.

Not available

S-EPMC6741141 | biostudies-literature

Molecular characterization of Calu-3 cells from submerged to Air-liquid interface to model lung infections

Air-liquid interface (ALI) model using the immortalized Calu-3 cells has been used to model lung diseases. From submerged to ALI culture condition, Calu-3 cells polarize and change to a ciliary mucus-producing cell. Polarized Calu-3 molecular and phenotypic similarity with primary cells has been pro...

ORGANISM(S): Homo sapiens (Human)

2026-02-23 | PXD056869 | Pride

Submerged differentiation of Aspergillus niger in carbon-limited cultures approaching zero specific growth rate

This work presents an exploration of submerged differentiation of the ubiquitous saprophyte and industrially important fungus, Aspergillus niger, in response to a limited availability of a sole carbon and energy source, maltose. In aspergilli and other mold fungi, asexual reproduction through format...

ORGANISM(S): Aspergillus niger

2010-07-07 | E-GEOD-21752 | biostudies-arrayexpress

Bioactivity assessment of exopolysaccharides produced by Pleurotus pulmonarius in submerged culture with different agro-waste residues.

Not available

S-EPMC7734227 | biostudies-literature

Optimization of Submerged Culture Parameters of the Aphid Pathogenic Fungus Fusarium equiseti Based on Sporulation and Mycelial Biomass.

Not available

S-EPMC9865567 | biostudies-literature

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