Co-cultures - OmicsDI

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Unknown (3936)
Transcriptomics (2628)
Genomics (1695)
Proteomics (310)
Metabolomics (72)
Other (16)
Models (2)
Methylation profiling (2)
Multiomics (1)

Organisms

Homo sapiens (1146)
Mus musculus (572)
Drosophila melanogaster (251)
Caenorhabditis elegans (239)
Saccharomyces cerevisiae (124)
Rattus norvegicus (58)
Escherichia coli (36)
Arabidopsis thaliana (34)
Rhizobium leguminosarum (26)
Schizosaccharomyces pombe (25)
Escherichia coli str. K-12 substr. MG1655 (24)
Streptomyces coelicolor (23)
Candida albicans (18)
Pseudomonas aeruginosa (18)
Escherichia coli K-12 (16)
Bos taurus (13)
Salmonella enterica subsp. enterica serovar Typhimurium (12)
Plasmodium falciparum (12)
Sus scrofa (9)
Bacillus subtilis (9)
Canis lupus familiaris (9)
Sinorhizobium meliloti (8)
Bacillus amyloliquefaciens (8)
Streptomyces coelicolor A3(2) (7)
Mycobacterium tuberculosis (7)
Ferroglobus placidus DSM 10642 (5)
Saccharomyces cerevisiae SK1 (5)
Bradyrhizobium japonicum (5)
Dictyostelium discoideum (5)
Haemophilus influenzae (5)

Organisms

Homo sapiens (461)
Mus musculus (190)
Saccharomyces cerevisiae (32)
Rattus norvegicus (14)
Nitratidesulfovibrio vulgaris str. Hildenborough (7)
Escherichia coli (7)
Bos taurus (6)
Synechocystis sp. PCC 6803 (5)
Dictyostelium discoideum (5)
Schizosaccharomyces pombe (5)
Arabidopsis thaliana (5)
Rattus (4)
Caenorhabditis elegans (4)
Pseudomonas aeruginosa (4)
Clostridium autoethanogenum (3)
Thalassiosira pseudonana (3)
Fusarium graminearum (3)
Candida albicans (3)
Staphylococcus aureus (3)
Danio rerio (3)
Plasmodium falciparum (3)
unidentified (3)
Trichodesmium erythraeum IMS101 (2)
Stenotrophomonas maltophilia K279a (2)
Streptococcus pneumoniae D39 (2)
Pseudomonas aeruginosa PA14 (2)
Streptococcus mutans UA159 (2)
Komagataella phaffii (2)
Penicillium chrysogenum (2)
Aspergillus nidulans (2)

Repository

biostudies-arrayexpress (2516)
ENA (1217)
geo (587)
pride (196)
MassIVE (77)
MetaboLights (53)
jPOST (32)
EGA (28)
GNPS (19)
iProX (5)
BioModels (2)
PAXDB (2)

Tissue

Cell culture (52)
Brain (11)
Fibroblast (11)
Cell suspension culture (9)
Epithelial cell (8)
Prokaryotic cell (7)
Lung (6)
Permanent cell line cell (6)
Plant cell (6)
T cell (5)
Blood (4)
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Monocyte (4)
Alveolar epithelial cell line (3)
Bone marrow (3)
Colon (3)
Epithelial cell of lung (3)
Mesothelial fibroblast (3)
Pleural mesothelium (3)
Astrocyte (2)
Cerebrospinal fluid (2)
Epithelial cell of cervix (2)
Fibroblast of lung (2)
Heart (2)
Keratinocyte (2)
Macrophage (2)
Photosynthetic cell (2)
Pluripotent stem cell (2)
Root (2)
B cell (1)

Disease

Breast cancer (12)
Normal (7)
Disease free (7)
Amyotrophic lateral sclerosis (3)
Colon cancer (3)
Lung adenocarcinoma (3)
Malignant pleural mesothelioma (3)
Plasmodium falciparum malaria (3)
Lung cancer (2)
Nurr1 lentivirus (1)
HIV-associated dementia (1)
Ovarian carcinoma (1)
Post-stasis (1)
Squamous cell carcinoma has accession C0007137 in DiseaseStateDatabase NCI_Thesaurus (1)
Severe acute respiratory syndrome (1)
Plasmodium berghei-infected cells (1)
Infiltrating ductal carcinoma (1)
Primary tumor (1)
Dukes D primary colon cancer (1)
Giant cell glioblastoma (1)
Colon cancer metastasis (1)
Rheumatoid arthritis (1)
Invasive lobular carcinoma (1)
Colorectal carcinoma (1)
Tumor (1)
Benign adenoma (1)
Chronic myelogenous leukemia (1)
Cancer (1)
Renal cell carcinoma (1)
N/a (1)

Technology Type

Mass Spectrometry (196)
Shotgun proteomics (95)
Bottom-up proteomics (44)
Mass spectrometry (37)
Data-dependent acquisition (25)
Data-independent acquisition (23)
Affinity purification coupled with mass spectrometry proteomics (21)
Gel-based experiment (15)
Mass spectrometry assay (11)
Top-down proteomics (8)
SRM/MRM (6)
NMR spectroscopy (5)
SWATH MS (5)
DiaPASEF (4)
Chemical cross-linking coupled with mass spectrometry proteomics (2)
Metaproteomics (2)
All-ion fragmentation (1)
HDMSE (1)

Instrument Platform

Illumina NovaSeq 6000 (94)
NextSeq 500 (53)
Illumina HiSeq 2500 (43)
Illumina HiSeq 2000 (39)
Illumina HiSeq 4000 (28)
Illumina Genome Analyzer IIx (12)
NextSeq 550 (12)
Illumina MiSeq (9)
NextSeq 2000 (8)
BGISEQ-500 (8)
Illumina NovaSeq X (7)
Racham server on Uppmax, NAISS (5)
FACS Aria-III (5)
GenePix 4000A [Axon Instruments] (4)
DNBSEQ-T7 (4)
BD FACSAria III cell sorter (3)
Axon- GenePix4000B (3)
G2565BA DNA microarray scanner [Agilent] (3)
GenePix 4000B [Axon Instruments] (3)
Vortex (3)
NextSeq 1000 (3)
NA (3)
Illumina HiSeq 1500 (3)
Illumina HiSeq 3000 (3)
Qubit 4.0 Fluorometer/ Agilen 5300 Fragment Analyzer (2)
Novogene in-house automated library preparation system (2)
Axon Instruments GenePix 4000B scanner (2)
2100 Bioanalyzer (2)
Agilent G2565AA and G2565BA Microarray Scanner (2)
GenePix Personal 4100A [Axon Instruments] (2)

Publication Date

2013 (401)
2010 (346)
2011 (340)
2015 (282)
2014 (232)
2012 (216)
2025 (213)
2026 (180)
2016 (174)
2024 (159)
2023 (128)
2020 (108)
2022 (105)
2021 (104)
2008 (101)
2009 (97)
2019 (70)
2018 (64)
2017 (56)
2007 (49)
2006 (32)
2005 (24)
2004 (3)
2003 (3)

UNIPROT ID/AC

1433S_HUMAN (2)
A0A087WXI2_HUMAN (2)
A0A096LPE2_HUMAN (2)
A1AG1_HUMAN (2)
A1AG2_HUMAN (2)
A1AT_HUMAN (2)
A1BG_HUMAN (2)
A2AP_HUMAN (2)
A2GL_HUMAN (2)
A2MG_HUMAN (2)
AACT_HUMAN (2)
ACTB_HUMAN (2)
ACTG_HUMAN (2)
ACTS_HUMAN (2)
ADIPO_HUMAN (2)
AFAM_HUMAN (2)
AGRG6_HUMAN (2)
ALBU_HUMAN (2)
ALS_HUMAN (2)
AMBP_HUMAN (2)
AMPN_HUMAN (2)
ANGT_HUMAN (2)
ANT3_HUMAN (2)
APMAP_HUMAN (2)
APOA1_HUMAN (2)
APOA2_HUMAN (2)
APOA4_HUMAN (2)
APOA_HUMAN (2)
APOB_HUMAN (2)
APOC1_HUMAN (2)

CHEBI ID

CHEBI:16708 (11)
CHEBI:15741 (11)
CHEBI:16335 (11)
CHEBI:15428 (9)
CHEBI:17750 (9)
CHEBI:17203 (9)
CHEBI:17822 (8)
CHEBI:25094 (8)
CHEBI:26986 (8)
CHEBI:17754 (8)
CHEBI:28044 (8)
CHEBI:30746 (8)
CHEBI:16865 (8)
CHEBI:17568 (8)
CHEBI:27266 (8)
CHEBI:16010 (8)
CHEBI:16027 (8)
CHEBI:16414 (8)
CHEBI:15603 (8)
CHEBI:30769 (8)
CHEBI:17992 (7)
CHEBI:26271 (7)
CHEBI:22660 (7)
CHEBI:24898 (7)
CHEBI:6650 (7)
CHEBI:17154 (7)
CHEBI:16449 (7)
CHEBI:18012 (7)
CHEBI:32816 (7)
CHEBI:27897 (7)

Metabolite Name

Taurine (8)
Adenosine (8)
Uridine (8)
L-Phenylalanine (8)
Hypoxanthine (8)
Uracil (7)
Thymine (7)
Fumaric acid (7)
Adenine (7)
Guanosine (7)
Thymidine (7)
Glycine (6)
Glycerol (6)
Trigonelline (6)
Valine (6)
Betaine (6)
Aspartame (6)
L-Histidine (6)
Citric acid (6)
Lysine (6)
Guanine (6)
L-Tryptophan (6)
Xanthine (6)
Sucrose (6)
L-Tyrosine (6)
Niacinamide (5)
Lumichrome (5)
Ornithine (5)
L-Threonine (5)
Pantothenic acid (5)

First Public Date

2014 (189)
2025 (176)
2024 (160)
2026 (157)
2023 (112)
2021 (80)
2022 (79)
2020 (75)
2017 (43)
2019 (40)
2018 (40)
2016 (28)
2015 (26)
2013 (12)

Modelling Approach

Other (1)
Agent-based model (1)

Lab affiliation

Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic (5)
University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry (4)
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain (3)
Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany (3)
Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Australia (2)
CRUK Beatson Institute (2)
Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain (2)
Department of Microbiology and Immunology, 299 Campus Drive, Stanford School of Medicine, Stanford CA 94305-5124 (2)
Koç University, Department of Molecular Biology and Genetic Cell Biology Lab head (2)
MRC Toxicology Unit, University of Cambridge (2)
University Clinic for Poultry and Fish Medicine, University of Veterinary Medicine, Vienna, Austria (2)
Wageningen University (2)
(1) Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; (2) VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium. (1)
1Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA 2Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA 3Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA (1)
1Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada 2Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada Departments of Biochemistry and Biology, Boston University, 71 E. Concord St, Boston, MA 02118, USA (1)
1Institute of Lung Health and Immunity, Comprehensive Pneumology Center Munich with the CPC-M bioArchive, Helmholtz Center Munich, Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), Germany (1)
2 Yuanmingyuan West Road, Haidian District, Beijing, P.R. China 100193Yuanmingyuan West Road, Haidian District, Beijing, P.R. China 100193 (1)
All India Institute of Medical Sciences, New Delhi, India (1)
Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland (1)
Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University Munich, Freising, Germany (1)
Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Canada (1)
Biochemistry, University of Turku, Turku, Finland (1)
Biomolecular Mass Spectrometry and Proteomics Utrecht University The Netherlands (1)
Biomolecular Mass Spectrometry and Proteomics, Utrecht University (1)
Biotech Research & Innovation Center (BRIC), University of Copenhagen, Denmark (1)
Boston University (1)
CCRI – St. Anna Children's Cancer Research Institute, Vienna, Austria Labdia - Labordiagnostik GmbH, Vienna, Austria Department of Pediatrics, Medical University of Vienna, Austria (1)
CERELA CONICET - Argentina (Reference Center for Lactobacilli, National Scientific and Technical Research Council - Argentina) (1)
CNRS, FRAIB, IPBS, France , Toulouse (1)
CSIC/UAB Proteomics Laboratory, IIBB-CSIC, Barcelona, Spain (1)

IsPrivate

False (2)

Submitter Keywords

Manuscript Accepted (1)

Classification

bacteria (49)
fungi (15)
protozoa (9)
viruses (1)

Modification

4x(2)H labeled dimethylated residue (1)
N6 (1)
N6-dimethyl-L-lysine (1)

Study type

Transcription profiling by array (1116)
ChIP-chip by tiling array (405)
ChIP-seq (390)
RNA-seq of coding RNA (251)
ChIP-chip by array (55)
RNA-seq of coding RNA from single cells (52)
Other (33)
Unknown experiment type (27)
Comparative genomic hybridization by array (26)
RNA-seq of non coding RNA (18)
Methylation profiling by array (17)
Cell line - High-throughput sequencing (16)
RNA-seq of total RNA (15)
Transcription profiling by tiling array (12)
DNA-seq (12)
Methylation profiling by high throughput sequencing (12)
Genotyping by array (9)
MicroRNA profiling by array (6)
Transcription profiling by SAGE (4)
Human - Single-cell sequencing (3)
High-throughput sequencing (3)
Animal - High-throughput sequencing (3)
RIP-seq (3)
Single nucleus RNA sequencing (3)
Human - One-color microarray (2)
MicroRNA profiling by high throughput sequencing (2)
ATAC-seq (2)
ChIP-chip by SNP array (1)
Cell line - Single-cell sequencing (1)
Differential (1)

Release Date

2013 (473)
2025 (457)
2022 (425)
2015 (420)
2023 (418)
2021 (413)
2011 (402)
2020 (399)
2024 (391)
2010 (383)
2014 (339)
2016 (326)
2019 (294)
2017 (291)
2012 (260)
2018 (257)
2009 (128)
2008 (122)
2026 (113)
2007 (61)
2006 (32)
2005 (27)
2004 (8)
2003 (5)
1999 (3)
2002 (2)
2001 (2)
2000 (1)

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Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion

Adaptive laboratory evolution has proven highly effective for obtaining microorganisms with enhanced capabilities. Yet, this method is inherently restricted to the traits that are positively linked to cell fitness, such as nutrient utilization. Here, we introduce coevolution of obligatory mutuali...

2021-07-02 | MTBLS2217 | MetaboLights

Enhanced photosynthetic CO2 fixation in mutualistic Chlorella sp. and Mesorhizobium loti co-cultures

It was further confirmed the stimulatory effect of M. loti-derived eCA on microalgae, highlighting key carbon metabolic pathways, including the Calvin cycle, TCA cycle and antioxidant defense response.

2025-01-20 | MTBLS11422 | MetaboLights

Transcriptome-based characterization of the interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in lactose-grown chemostat co-cultures

The present study aims to explore chemostat-based transcriptome analysis of mixed cultures by investigating interactions between the yeast S. cerevisiae and the lactic acid bacterium Lb. bulgaricus . S. cerevisiae and Lb. bulgaricus are both frequently encountered in kefir, a fermented dairy product...

ORGANISM(S): Saccharomyces cerevisiae

2013-08-22 | E-GEOD-45776 | biostudies-arrayexpress

Expression data from HT29 intestinal epithelial cell line

The study recapitulates, through in vitro micropatterned co-cultures, interactions between HIV-infected T-lymphocytes and intestinal epithelial cells in order to investigate the mechanisms underlying the disruption of normal epithelial cell and barrier function during HIV infection. The co-culture m...

ORGANISM(S): Homo sapiens

2014-03-22 | E-GEOD-56090 | biostudies-arrayexpress

Co-cultures of enteric neurons and T cells

PRJNA691242 | ENA

Single-cell profiling of co-cultures of GSCCs and macrophages

Glioblastoma (GBM) remains the most malignant primary brain tumor, with a median survival rarely exceeding 2 years. Tumor heterogeneity and an immunosuppressive microenvironment are key factors contributing to the poor response rates of current therapeutic approaches. GBM-associated macrophages (GAM...

EGAS00001007482 | EGA

Non-targeted metabolomics of Gut bacterial co-cultures

Non-targeted metabolomics analysis of cell and medium extract obtained by bacterial co-cultures.

ORGANISM(S): Environmental Samples <bacillariophyta> (ncbitaxon:33858)

2023-03-09 | MSV000091452 | MassIVE

Expression data from prostate cancer and osteoblast co-cultures

PRJNA296005 | ENA

RNA-seq of air-liquid interface co-cultures of A549 and THP-1 cells exposed to Saharan dust or DQ12 against unexposed controls

Although desert dust is known to cause increased respiratory morbidity and mortality, the underlying biological pathways remain unclear. We used RNA-seq on an advanced human alveolar in vitro model to find yet unidentified genes dysregulated by Saharan dust exposure. For comparison, DQ12 quartz dust...

ORGANISM(S): Homo sapiens

2024-03-15 | E-MTAB-13372 | biostudies-arrayexpress

Tissue-resident memory T cells- iPSC-cardiomyocyte co-cultures

PRJNA1079821 | ENA

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