Yamada S S - OmicsDI

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Unknown (4375)
Transcriptomics (135)
Proteomics (46)
Metabolomics (27)
Genomics (13)
Models (2)

Organisms

Homo sapiens (56)
Mus musculus (38)
Corynebacterium glutamicum ATCC 13032 (19)
Arabidopsis thaliana (16)
Corynebacterium glutamicum (15)
Rattus norvegicus (10)
Daphnia pulex (9)
Ciona intestinalis (2)
Schizosaccharomyces pombe (2)
Saccharomyces cerevisiae (2)
Streptomyces coelicolor (2)
Bombyx mori (2)
Ralstonia solanacearum (1)
Rattus rattus (1)
Oryza sativa Japonica Group (1)
Lactuca sativa (1)
cellular organisms (1)
Akkermansia muciniphila ATCC BAA-835 (1)
Escherichia coli (1)
Lingula anatina (1)
Mycoplasmoides pneumoniae M129 (1)
Oryza sativa (1)
Phytomonas serpens (1)
Roseburia hominis A2-183 (1)
Roseburia inulinivorans DSM 16841 (1)
Streptococcus pyogenes M1 GAS (1)
Trypanosoma cruzi Dm28c (1)
Trypanosoma rangeli (1)

Organisms

Mus musculus (2)
Streptomyces coelicolor (1)
Rattus norvegicus (1)
Homo sapiens (1)

Repository

biostudies-arrayexpress (139)
MetaboLights (27)
pride (22)
jPOST (19)
ENA (5)
geo (4)
MassIVE (4)
BioModels (2)
iProX (1)

Tissue

Epithelial cell (3)
Plant cell (3)
Cell culture (2)
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Pancreas (1)
Root (1)
Rosette (1)
Seedling (1)
Shoot meristem (1)
Stem cell (1)

Disease

Osteosarcoma subtype fibroblastic (1)
Cardiovascular system disease (1)
Ehlers-Danlos syndrome classic type 1 (1)
Malignant neoplasm of ovary (1)
Ovary epithelial cancer (1)
Severe acute respiratory syndrome (1)

Technology Type

Mass spectrometry (26)
Mass Spectrometry (22)
Shotgun proteomics (14)
Bottom-up proteomics (3)
Gel-based experiment (3)
Affinity purification coupled with mass spectrometry proteomics (2)
Data-dependent acquisition (2)
SRM/MRM (2)
Mass spectrometry assay (1)
NMR spectroscopy (1)
All-ion fragmentation (1)

Instrument Platform

Liquid Chromatography MS - positive - reverse phase (13)
Liquid Chromatography MS - negative - reverse phase (9)
Agilent High resolution C scanner (4)
Illumina HiSeq 1500 (3)
Capillary electrophoresis MS - negative (3)
Capillary electrophoresis MS - positive (3)
Liquid Chromatography MS - Positive (LC-MS (Positive)) (3)
Illumina MiSeq (2)
NextSeq 550 (2)
Illumina HiSeq 2500 (2)
Liquid Chromatography MS - Negative (LC-MS (Negative)) (2)
Liquid Chromatography MS - alternating - reverse phase (2)
Liquid Chromatography MS - positive - hilic (2)
GenePix 4000B [Axon Instruments] (1)
Illumina NovaSeq 6000 (1)
Illumina HiSeq 4000 (1)
NextSeq 500 (1)
LTQ Orbitrap Velos (1)
Orbitrap Ascend (1)
Q Exactive (1)
Q Exactive Plus (1)
LTQ Orbitrap Velos (Thermo Scientific) (1)
Liquid Chromatography MS - - reverse phase (1)
Liquid Chromatography MS - alternating - hilic (1)
Liquid Chromatography MS - negative - hilic (1)
Liquid Chromatography MS - negative - reverse-phase (1)
Liquid Chromatography MS - positive - reverse-phase (1)
MicrOTOF-Q II ESI-Qq-TOF (Bruker) (1)
Nuclear Magnetic Resonance (NMR) - (1)
Xevo G2 QTOF (Waters) (1)

Publication Date

2013 (24)
2010 (20)
2016 (16)
2011 (16)
2014 (14)
2023 (14)
2015 (13)
2012 (12)
2022 (12)
2024 (11)
2020 (11)
2025 (10)
2021 (9)
2008 (9)
2009 (7)
2019 (5)
2026 (4)
2005 (3)
2018 (2)
2007 (2)
2017 (2)
2006 (1)
2004 (1)

UNIPROT ID/AC

O35716 (2)
P01572 (2)
P35235 (2)
P42225 (2)
P52332 (2)
O88507 (1)
P15261 (1)

CHEBI ID

CHEBI:16335 (10)
CHEBI:17750 (10)
CHEBI:16708 (9)
CHEBI:17509 (9)
CHEBI:15354 (8)
CHEBI:15676 (8)
CHEBI:16235 (8)
CHEBI:16704 (8)
CHEBI:16919 (8)
CHEBI:17596 (8)
CHEBI:17895 (8)
CHEBI:17929 (8)
CHEBI:73024 (8)
CHEBI:15682 (7)
CHEBI:15741 (7)
CHEBI:16040 (7)
CHEBI:16680 (7)
CHEBI:16737 (7)
CHEBI:16750 (7)
CHEBI:16765 (7)
CHEBI:16811 (7)
CHEBI:17154 (7)
CHEBI:17310 (7)
CHEBI:17368 (7)
CHEBI:17405 (7)
CHEBI:17562 (7)
CHEBI:17568 (7)
CHEBI:17752 (7)
CHEBI:17822 (7)
CHEBI:33699 (2)

Metabolite Name

Adenine (6)
Adenosine (6)
Allantoin (5)
Betaine (5)
Creatine (5)
Creatinine (5)
Guanine (5)
Hypoxanthine (5)
Inosine (5)
Methionine sulfoxide (5)
Uracil (5)
Xanthine (5)
Acetylcholine (4)
Asparagine (4)
Biotin (4)
Choline (4)
Cytidine (4)
Cytosine (4)
Histamine (4)
Kynurenic acid (4)
Pantothenic acid (4)
Pyridoxal (4)
Serotonin (4)
Trigonelline (4)
Tryptamine (4)
Uridine (4)
2-Aminophenol (3)
2-Quinolinecarboxylate (3)
3-Hydroxybutyrate (3)
4-Pyridoxate (3)

First Public Date

2014 (4)
2023 (1)

Modelling Approach

Ordinary differential equation model (2)

Lab affiliation

Brigham and Women's Hospital, Harvard Medical School (1)
Carlos Chagas Institute, Fiocruz Parana, Brazil (1)
Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Carrer Dr. Aiguader 88, Barcelona 08003, Spain. (1)
DTU BIOENGINEERING Department of Biotechnology and Biomedicine PCET-Protein Glycoscience and Biotechnology Technical University of Denmark 2800 Kgs. Lyngby (1)
Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan. (1)
Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, 95616, USA (1)
Department of Systems Pharmacology, Graduate School of Medicine, the University of Tokyo, Japan (1)
Immunopathology of Virus Infections Institute of Virology Technical University of Munich Schneckenburgerstr. 8 D-81675 Munich, Germany tel: +49 (0) 89 4140 9270 (1)
Instituto de Bioquímca Vegetal y Fotosíntesis-CSIC Avda. Américo Vespucio, 49 41092-Sevilla Spain (1)
Kihara Institute for Biological Research, Yokohama City University (1)
Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Japan (1)
Max Planck Institute of Biochemistry Department of Proteomics and Signaltransduction Am Klopferspitz 18 D-82152 Martinsried (1)
Mayo Clinic Center for Regenerative Medicine Department of Cardiovascular Medicine Rochester, MN, USA (1)
Molecular Bacteriology (1)
Plant Molecular Biology Lab, Malopolska Centre of Biotechnology, Jagiellonian University (1)
Plant Molecular Biology Laboratory, Malopolska Centre of Biotechnology, Jagiellonian Univerisity (1)
Principle Investigator (1)
Proteome Research (AG Stühler) Heinrich Heine University Düsseldorf Universitätsstraße 1 40225 Düsseldorf Germany (1)
Proteomics and Signal Transduction Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried, Germany (1)
Shinshu University (1)
TOR center, Department of Dentistry, Uinversity Of Bergen, Norway (1)
University of Illinois at Chicago, College of Medicine (1)

IsPrivate

False (2)

Modification

15.994915 (1)
57.021464 (1)
79.966331 (1)

Study type

Transcription profiling by array (87)
Unknown experiment type (9)
RNA-seq of coding RNA (7)
ChIP-seq (6)
ChIP-chip by array (5)
ChIP-chip by tiling array (4)
Transcription profiling by tiling array (4)
Animal - One-color microarray (3)
High-throughput sequencing (2)
RIP-seq (2)
Transcription profiling by SAGE (1)
Plant - One-color microarray (1)
RNAi profiling by array (1)
Genotyping by array (1)
Transcription profiling by RT-PCR (1)
Other (1)
DNA-seq (1)
Methylation profiling by array (1)
RNA-seq of coding RNA from single cells (1)
Methylation profiling by high throughput sequencing (1)

Release Date

2022 (486)
2021 (462)
2023 (429)
2025 (409)
2024 (390)
2020 (329)
2019 (310)
2018 (260)
2017 (205)
2016 (188)
2015 (173)
2014 (152)
2013 (108)
2011 (91)
2012 (89)
2010 (82)
2026 (78)
2009 (63)
2008 (46)
2007 (34)
2005 (20)
2003 (19)
2006 (18)
2004 (15)
2001 (14)
2000 (13)
2002 (12)
1999 (12)
1998 (5)
1997 (2)

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S. coelicolor M752 SMM medium time course study

Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study,...

ORGANISM(S): Streptomyces coelicolor

2010-10-25 | E-GEOD-22398 | biostudies-arrayexpress

Genome-wide localization of ORC and MCM binding sites and identification of replication origins in S. pombe

DNA replication of eukaryotic chromosomes initiates at a number of discrete loci, called replication origins. Distribution and regulation of origins are important for complete duplication of the genome. Here, we determined locations of Orc1 and Mcm6, components of pre-replicative complex (pre-RC),...

ORGANISM(S): Schizosaccharomyces pombe

2010-06-11 | E-GEOD-6523 | biostudies-arrayexpress

Histone H3 lysine9 acetylation, rather than lysine4 trimethylation, marks meiotic recombination hotspots and promotes recombination initiation in fission yeast

Histone modifications are associated with meiotic recombination hotspots, discrete sites with augmented recombination frequency. For example, trimethylation of histone H3 lysine4 (H3K4me3) marks most hotspots in budding yeast and mouse. Modified histones are known to regulate meiotic recombinatio...

ORGANISM(S): Schizosaccharomyces pombe

2013-03-07 | E-GEOD-31648 | biostudies-arrayexpress

S. coelicolor M752 SMM medium time course study

ORGANISM(S): Streptomyces coelicolor

2010-10-25 | GSE22398 | GEO

Inhibitory effect of toothbrush monofilament containing surface pre-reacted glass-ionomer (S-PRG) filler on Streptococcus mutans.

Not available

S-EPMC7794465 | biostudies-literature

Occurrence of Cis-11,12-Methylene-Hexadecanoic Acid in the Red Alga Solieria pacifica (Yamada) Yoshida.

Not available

S-EPMC8071341 | biostudies-literature

Anti-Alzheimer's Disease Activity of Bromophenols from a Red Alga, Symphyocladia latiuscula (Harvey) Yamada.

Not available

S-EPMC6682041 | biostudies-literature

PIG-S and PIG-T, essential for GPI anchor attachment to proteins, form a complex with GAA1 and GPI8.

Not available

S-EPMC149153 | biostudies-literature

Oxygen-evolving photosystem II structures during S₁-S₂-S₃ transitions.

Not available

S-EPMC10866707 | biostudies-literature

Primary human neuroblastoma

Reference1: Ohira M, Oba S, Nakamura Y, Isogai E, Kaneko S, Nakagawa A, Hirata T, Kubo H, Goto T, Yamada S, Yoshida Y, Fuchioka M, Ishii S, Nakagawara A. Expression profiling of human primary Expression profiling using a tumor-specific cDNA microarray predicts the prognosis of intermediate risk neur...

ORGANISM(S): Homo sapiens

2005-05-12 | E-GEOD-2283 | biostudies-arrayexpress

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4598 Results

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