Culture ks - OmicsDI

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Unknown (1023)
Transcriptomics (129)
Proteomics (106)
Genomics (31)
Metabolomics (6)
Models (1)

Organisms

Homo sapiens (45)
Mus musculus (26)
Rattus norvegicus (13)
Escherichia coli (11)
Nicotiana tabacum (3)
Caenorhabditis elegans (3)
Escherichia coli K-12 (3)
Arabidopsis thaliana (3)
Yersinia pestis (2)
Escherichia coli str. K-12 substr. MG1655 (2)
cellular organisms (1)
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mixed sample (1)

Organisms

Yersinia pestis CO92 (1)
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Ferrigenium straubiae (1)
Comamonas thiooxydans (1)
Cricetulus griseus (1)
freshwater sediment metagenome (1)
Rattus norvegicus (1)
Plasmodium falciparum (1)
Mus musculus (1)

Repository

biostudies-arrayexpress (142)
pride (105)
ENA (21)
MetaboLights (6)
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Tissue

Cell culture (65)
Epithelial cell (19)
Cell suspension culture (8)
Brain (6)
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Root (3)
Callus culture (2)
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T cell (2)
Adult organism (1)
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Blood (1)
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Blood plasma (1)
HEK-293T cell (1)
NCI-H295R cell (1)

Disease

Malignant neoplasm of ovary (9)
Glioblastoma (5)
Breast cancer (3)
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Melanoma (2)
Trypanosomiasis (2)
AIDS-KS, HIV+, nodular (late) stage (1)
Adenocarcinoma (1)
Normal (1)
Acute leukemia (1)
Alzheimer's disease (1)
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Blastic plasmacytoid dendritic cell neoplasm (1)
Bone osteosarcoma (1)
Brain cancer (1)
COVID-19 (1)
Cancer (1)
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Chordoma (1)
Chronic kidney disease (1)
Kaposi's sarcoma (1)
Leishmaniasis (1)
Lymphoma (1)
Neuroblastoma (1)
Parkinson's disease 1 (1)
Retinal degeneration (1)
Severe acute respiratory syndrome (1)

Technology Type

Mass Spectrometry (105)
Shotgun proteomics (65)
Affinity purification coupled with mass spectrometry proteomics (21)
Bottom-up proteomics (15)
Data-dependent acquisition (10)
Gel-based experiment (9)
Data-independent acquisition (7)
SWATH MS (6)
HDMSE (5)
Mass spectrometry (4)
NMR spectroscopy (1)
Mass spectrometry assay (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)
MSE (1)
SRM/MRM (1)
Top-down proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (7)
Illumina HiSeq 4000 (5)
Illumina HiSeq 2000 (3)
NextSeq 500 (3)
Infors HT Multitron shaker (2)
Illumina HiSeq 2500 (2)
Liquid Chromatography MS - positive - reverse phase (2)
Described in protocol (1)
MACS (1)
Not applicable (1)
GenePix Professional 4200A [Axon Instruments] (1)
ScanArray Express HT [PerkinElmer] (1)
GenePix 4000B [Axon Instruments] (1)
Illumina NovaSeq X (1)
NextSeq 2000 (1)
Illumina HiSeq 1000 (1)
Illumina MiSeq (1)
Illumina HiSeq 1500 (1)
Gas Chromatography MS - positive - medium polarity - Agilent 6890 GC - LECO Pegasus III TOF MS (LECO) (1)
Agilent 5975E GC/MSD (Agilent) (1)
Liquid Chromatography MS - - reverse phase (1)
Bruker (1)
Liquid Chromatography MS - negative - reverse phase (1)

Publication Date

2012 (24)
2022 (20)
2015 (19)
2024 (18)
2016 (17)
2025 (15)
2023 (15)
2011 (15)
2010 (15)
2026 (13)
2020 (12)
2019 (11)
2014 (11)
2021 (10)
2013 (8)
2018 (7)
2008 (6)
2007 (5)
2017 (4)
2009 (4)
2006 (3)
2005 (1)
2004 (1)

UNIPROT ID/AC

P47736 (1)
Q62636 (1)
P10113 (1)
Q9QYV3 (1)
P47196 (1)
P47197 (1)
P63086 (1)
P21708 (1)
P36506 (1)
Q01986 (1)
Q99MC6 (1)
P11345 (1)
P50904 (1)
Q9Z1I2 (1)
Q63531 (1)
Q9Z1I1 (1)
P35739 (1)
P25427 (1)
Q63484 (1)
Q9QX70 (1)
P07522 (1)

ENSEMBL ID

ENSRNOP00000009359 (1)

CHEBI ID

CHEBI:17234 (4)
CHEBI:28300 (4)
CHEBI:15428 (4)
CHEBI:17822 (3)
CHEBI:22660 (3)
CHEBI:18186 (3)
CHEBI:26986 (3)
CHEBI:15741 (3)
CHEBI:6650 (3)
CHEBI:28044 (3)
CHEBI:27266 (3)
CHEBI:16449 (3)
CHEBI:27897 (3)
CHEBI:26078 (3)
CHEBI:15756 (3)
CHEBI:30769 (3)
CHEBI:15361 (2)
CHEBI:24266 (2)
CHEBI:17521 (2)
CHEBI:17992 (2)
CHEBI:27386 (2)
CHEBI:15584 (2)
CHEBI:26984 (2)
CHEBI:33508 (2)
CHEBI:59783 (2)
CHEBI:27693 (2)
CHEBI:16680 (2)
CHEBI:26271 (2)
CHEBI:18132 (2)
CHEBI:25094 (2)

Metabolite Name

Glyceric acid (2)
1,6-anhydroglucose (2)
Glutamic acid (2)
Aspartic acid (2)
Tryptophan (2)
Serine (2)
Lysine (2)
Phenylalanine (2)
Threonine (2)
Glucose (2)
Glutamine (2)
Glycine (2)
Citric acid (2)
Glycerol (2)
Sucrose (2)
Succinic acid (2)
Malic acid (2)
Pyruvate (2)
(+-)-Baclofen (1)
(3E)-3-Benzylidene-4-Methyl-1H-1,4-Benzodiazepine-2,5-Dione (1)
(5R)-5-Hydroxy-1-(4-Hydroxy-3-Methoxyphenyl)Tetradecan-3-One (1)
1,2-Dihydroxyheptadec-16-En-4-Yl Acetate (1)
2,5-Dihydroxy-3-Undecylcyclohexa-2,5-Diene-1,4-Dione (1)
2-Naphthalene Sulfonic Acid (1)
3-Indoxyl Sulfate (1)
3-Phospho-D-Glycerate (1)
3-Sulfino-L-Alanine (1)
4,4`-Thiodiphenol (1)
4-Methylumbelliferyl Sulfate (1)
5,10-Dimethoxy-2,2-Dimethylpyrano[3,2-G]Chromen-8-One (1)

First Public Date

2026 (4)
2021 (4)
2025 (3)
2024 (2)
2020 (2)
2019 (2)
2014 (2)
2018 (1)
2017 (1)

Modelling Approach

Ordinary differential equation model (1)

Lab affiliation

MRC Toxicology Unit, University of Cambridge, UK (4)
Head of System Biology Lab. at Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Russia (3)
DZNE Munich, Neuroproteomics, Feodor-Lynen-Str. 17, 81377 München, Germany (2)
Department of Biochemistry, University of Cambridge (2)
Department of Biochemistry, University of Cambridge, UK (2)
Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea (2)
MRC Toxicology Unit, University of Cambridge (2)
Molecular Oncology Chemical Biology and Molecular Medicine Moffitt Cancer Center & Research Institute, SRB3 12902 Magnolia Drive, Tampa, FL, 33612, USA. (2)
System Biology Laboratory at Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency (2)
Systems Biology Laboratory, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency (2)
ARC Centre of Excellence in Plant Cell Walls School of BioSciences The University of Melbourne Australia (1)
Aix Marseille Univ, CNRS, BIP, UMR7281, IMM, FR3479 (1)
Analytical Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy (1)
Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany (1)
Biological Sciences Division, Pacific Northwest National Laboratory (1)
Biomedical Research Institute, Foundation for Research and Technology-Hellas, Ioannina, Greece. (1)
British Antarctic Survey High Cross, Madingley Rd, Cambridge, CB3 0ET (1)
Brunel University London (1)
Cambridge Centre for Proteomics Cambridge System Biology Centre Wellcome Trust Stem Cell building University of Cambridge Department of Biochemistry Tennis Court Road Cambridge CB2 1QR (1)
Cambridge Centre for Proteomics University of Cambridge (1)
Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, U.K. (1)
Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge (1)
Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK (1)
Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, UK (1)
Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, United Kingdom (1)
Cambridge University (1)
Center for Theragnosis, Korea Institute of Science and Technology, Seoul, Korea (1)
Centre de Recherche en Cancérologie de Marseille, CRCM Inserm UMR1068, CNRS UMR7258, Aix Marseille Université U105, Institut Paoli Calmettes 27 Boulevard Leï Roure CS30059 13273 Marseille Cedex 09 France (1)
Centre to Impact AMR, Monash University; Clayton, 3800, Australia Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University; Clayton, 3800, Australia (1)
Charité Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany (1)

IsPrivate

False (1)

Classification

protozoa (1)
bacteria (1)

Study type

Transcription profiling by array (85)
RNA-seq of coding RNA (20)
RNA-seq of coding RNA from single cells (8)
ChIP-seq (7)
Unknown experiment type (4)
Other (4)
DNA-seq (3)
Genotyping by array (2)
Cell line - Single-cell sequencing (1)
ChIP-chip by tiling array (1)
Transcription profiling by RT-PCR (1)
Single nucleus RNA sequencing (1)
Proteomic profiling by array (1)
RNA-seq of total RNA (1)
RNA-seq of non coding RNA (1)

Release Date

2022 (104)
2023 (94)
2021 (94)
2025 (87)
2020 (83)
2024 (81)
2018 (79)
2019 (68)
2016 (67)
2015 (61)
2017 (59)
2012 (48)
2014 (46)
2013 (40)
2011 (36)
2010 (36)
2009 (19)
2008 (16)
2026 (13)
2007 (12)
2006 (7)
2004 (5)
2005 (3)
2002 (3)
2000 (2)
2001 (1)
1996 (1)

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LC-MS/MS of autotrophic culture KS, that performs nitrate reduction coupled to iron(II) oxidation (NDFO)

Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly under...

ORGANISM(S): freshwater sediment metagenome

2021-05-17 | PXD023186 | Pride

Transcription profiling of Kaposi sarcoma, normal skin and primary cells

Identification of the relationships of Kaposi sarcoma (KS), normal skin to various cell cultures. The effects of KS herpes virus, the infectious cause of KS, on infected endothelial cells are also investigated.

ORGANISM(S): Homo sapiens

2004-08-01 | E-MEXP-66 | biostudies-arrayexpress

Metagenomic Analyses of the Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture KS.

Not available

S-EPMC4836422 | biostudies-literature

Insights into Nitrate-Reducing Fe(II) Oxidation Mechanisms through Analysis of Cell-Mineral Associations, Cell Encrustation, and Mineralogy in the Chemolithoautotrophic Enrichment Culture KS.

Not available

S-EPMC5478975 | biostudies-literature

Metabolic Performance and Fate of Electrons during Nitrate-Reducing Fe(II) Oxidation by the Autotrophic Enrichment Culture KS Grown at Different Initial Fe/N Ratios.

Not available

S-EPMC10057050 | biostudies-literature

Meta-omics Reveal Gallionellaceae and Rhodanobacter Species as Interdependent Key Players for Fe(II) Oxidation and Nitrate Reduction in the Autotrophic Enrichment Culture KS.