Chen Run R - OmicsDI

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Unknown (539)
Proteomics (174)
Transcriptomics (138)
Metabolomics (52)
Genomics (43)

Organisms

Homo sapiens (161)
Mus musculus (75)
Rattus norvegicus (28)
Schizosaccharomyces pombe (21)
Drosophila melanogaster (7)
Arabidopsis thaliana (5)
Aggregatibacter actinomycetemcomitans (2)
Rattus rattus (2)
Sus scrofa (2)
Anser cygnoides (2)
Capsicum annuum (2)
Escherichia coli (2)
Solanum lycopersicum (2)
Sus scrofa domesticus (2)
Heliconius erato etylus x Heliconius himera (1)
Drosophila mojavensis (1)
Cucumis sativus (1)
Oryza sativa Indica Group (1)
Hordeum vulgare (1)
Glycine max (1)
Caenorhabditis elegans (1)
Saccharomyces cerevisiae (1)
Candida albicans (1)
Acinetobacter baumannii AB_TG2631 (1)
Arachis hypogaea (1)
Bacillus thuringiensis serovar kurstaki str. HD73 (1)
Bacteria (1)
Candidatus Lokiarchaeum ossiferum (1)
Coffea arabica (1)
Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (1)

Organisms

Homo sapiens (1)

Repository

pride (167)
biostudies-arrayexpress (147)
MetaboLights (51)
EGA (33)
MassIVE (3)
iProX (2)
PeptideAtlas (2)
GNPS (1)
ENA (1)

Tissue

Cell culture (46)
Epithelial cell (9)
Blood plasma (8)
Brain (8)
Blood serum (6)
Leaf (6)
Whole body (6)
B cell (5)
Blood (5)
Permanent cell line cell (5)
T cell (5)
Bone marrow (4)
Plant cell (4)
Breast (3)
Embryonic stem cell (3)
Heart (3)
Liver (3)
Neutrophil (3)
Root (3)
Sperm (3)
Plasma Non-glyco (2)
Cell suspension culture (2)
Dental plaque (2)
Early embryonic cell (2)
Fibroblast (2)
Fruit (2)
Hepatocyte (2)
Iris (2)
JURKAT cell (2)
Kidney (2)

Disease

Disease free (5)
Acute leukemia (4)
Breast cancer (4)
Malignant neoplasm of ovary (3)
COVID-19 (2)
Lymphoma (2)
Type 2 diabetes mellitus (2)
Hepatocellular carcinoma-non tumorous region (1)
Small cell lung carcinoma (1)
Alzheimer's disease (1)
Amyotrophic lateral sclerosis (1)
Bacterial meningitis (1)
Bone osteosarcoma (1)
Brain cancer (1)
Brain glioblastoma multiforme (1)
Cardiovascular system disease (1)
Cervix carcinoma (1)
Colon cancer (1)
Dental caries (1)
Diffuse gastric cancer (1)
Diffuse midline glioma (1)
Fibromyalgia (1)
Frontotemporal dementia (1)
Immune system disease (1)
Influenza (1)
Kidney cancer (1)
Lung cancer (1)
Melanoma (1)
Non-small cell lung carcinoma (1)
Oligodendroglioma (1)

Technology Type

Mass Spectrometry (167)
Shotgun proteomics (96)
Mass spectrometry (48)
Bottom-up proteomics (28)
Affinity purification coupled with mass spectrometry proteomics (17)
Gel-based experiment (12)
Data-dependent acquisition (10)
Data-independent acquisition (10)
SWATH MS (9)
Top-down proteomics (5)
Mass spectrometry assay (2)
Chemical cross-linking coupled with mass spectrometry proteomics (2)
MSE (2)
NMR spectroscopy (1)
Affinity proteomics (1)
All-ion fragmentation (1)
DiaPASEF (1)
Glycoproteomics (1)
Mass spectrometry imaging (1)
RNA mass spectrometry (1)
SRM/MRM (1)

Instrument Platform

Liquid Chromatography MS - positive - reverse phase (21)
Liquid Chromatography MS - negative - reverse phase (16)
Liquid Chromatography MS - negative - hilic (7)
Q Exactive (6)
Liquid Chromatography MS - positive - hilic (6)
Axon GenePix 4000B scanning hardware (4)
Illumina HiSeq 2500 (4)
Gas Chromatography MS - positive (3)
Illumina Genome Analyzer (2)
Illumina Genome Analyzer II (2)
Illumina NovaSeq 6000 (2)
Gas Chromatography MS - Positive (GC-MS (Positive)) (2)
Liquid Chromatography MS - Positive (LC-MS (Positive)) (2)
Liquid Chromatography MS - alternating - reverse phase (2)
454 GS 20 (1)
Scanning hardware (1)
Illumina HiSeq 2000 (1)
Illumina HiSeq 4000 (1)
NextSeq 500 (1)
Q Exactive Plus (1)
LTQ (1)
LTQ Orbitrap Elite (1)
API 4000 QTRAP (AB Sciex) (1)
API 5500 QTRAP (AB Sciex) (1)
Agilent 5975E GC/MSD (Agilent) (1)
Capillary electrophoresis MS - negative (1)
Capillary electrophoresis MS - positive (1)
Exactive (Thermo Scientific) (1)
LTQ Orbitrap Velos (Thermo Scientific) (1)
Liquid Chromatography MS - (1)

Publication Date

2022 (36)
2023 (30)
2021 (29)
2025 (27)
2024 (25)
2010 (23)
2020 (21)
2005 (20)
2015 (17)
2026 (17)
2018 (15)
2011 (14)
2019 (14)
2016 (13)
2014 (12)
2013 (12)
2004 (12)
2017 (8)
2009 (8)
2008 (6)
2007 (6)
2012 (4)
2006 (4)

UNIPROT ID/AC

A0A024RC46 (2)
A0A0B4J220 (2)
A5A3E0 (2)
A6NCN2 (2)
A6NNZ2 (2)
B3KML9 (2)
B3KT93 (2)
B4DRV9 (2)
B4E3A4 (2)
C9JM50 (2)
C9JRZ8 (2)
C9JZR2 (2)
E7EX29 (2)
E9PB61 (2)
E9PKG0 (2)
E9PRG8 (2)
G5E972 (2)
G8JLB6 (2)
H0Y5B0 (2)
H0Y804 (2)
H0YAR2 (2)
H0YDN1 (2)
H0YJH7 (2)
H0YM50 (2)
I3L4N8 (2)
J3QRK5 (2)
J9JID7 (2)
K7EJJ5 (2)
M0QY37 (2)
O00148 (2)

ENSEMBL ID

ENSG00000170477 (2)
ENSG00000247315 (1)

CHEBI ID

CHEBI:15354 (19)
CHEBI:16704 (18)
CHEBI:17368 (18)
CHEBI:17596 (18)
CHEBI:27897 (17)
CHEBI:30769 (17)
CHEBI:15891 (16)
CHEBI:16750 (16)
CHEBI:28044 (16)
CHEBI:16335 (15)
CHEBI:16708 (15)
CHEBI:17568 (15)
CHEBI:18237 (15)
CHEBI:6650 (15)
CHEBI:15318 (14)
CHEBI:17533 (14)
CHEBI:17750 (14)
CHEBI:18186 (14)
CHEBI:28790 (14)
CHEBI:15428 (13)
CHEBI:16010 (13)
CHEBI:16610 (13)
CHEBI:16811 (13)
CHEBI:16919 (13)
CHEBI:17154 (13)
CHEBI:17234 (13)
CHEBI:17822 (13)
CHEBI:18012 (13)
CHEBI:18211 (13)
CHEBI:18257 (13)

Metabolite Name

Hypoxanthine (10)
Inosine (10)
Taurine (9)
Uracil (9)
Uridine (9)
Spermidine (8)
Xanthine (8)
Adenine (7)
Adenosine (7)
Choline (7)
Creatine (7)
Guanosine (7)
Indole (7)
Phenylalanine (7)
Riboflavin (7)
Thymine (7)
2-aminoadipate (6)
Arachidonic acid (6)
Benzaldehyde (6)
Cytidine (6)
Histamine (6)
L-Ornithine (6)
Leucine (6)
Lysine (6)
Methionine (6)
N-acetylglutamate (6)
N-acetylputrescine (6)
N6-acetyllysine (6)
Nicotinamide (6)
Sarcosine (6)

First Public Date

2025 (1)

Study type

Transcription profiling by array (94)
RNA-seq of coding RNA (28)
ChIP-seq (8)
Unknown experiment type (3)
Comparative genomic hybridization by array (2)
Methylation profiling by array (2)
RNA-seq of non coding RNA (2)
ChIP-chip by tiling array (1)
Transcription profiling by tiling array (1)
Bisulfite-seq (1)
ATAC-seq (1)
Other (1)
DNA-seq (1)
RNA-seq of coding RNA from single cells (1)
RNA-seq of total RNA (1)

Release Date

2025 (112)
2024 (91)
2023 (79)
2022 (79)
2021 (52)
2020 (35)
2019 (25)
2010 (24)
2005 (22)
2015 (20)
2016 (17)
2011 (17)
2026 (16)
2014 (15)
2013 (15)
2018 (14)
2004 (12)
2017 (11)
2009 (9)
2008 (6)
2007 (6)
2012 (5)
2006 (4)

Lab affiliation

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA (4)
1) Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX 77030, USA 2) Proteomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX 77030, USA 3) Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX 77030, USA (2)
Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China (2)
Shanghai Jiao Tong University Affiliated Sixth People's Hospital (2)
UMR_S1134 Inserm/Université Paris Cité, Paris, France (2)
Yale University (2)
1 Health Management Center, the Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, China; 2 Department of Cardiology, the Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, China; (1)
1Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD (1)
1Gavin Herbert Eye Institute –Brunson Center for Translational Vision Research, Department of Ophthalmology and Visual Sciences, University of California Irvine, Irvine, CA 92697, USA 2Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA 3Department of Chemistry, University of California Irvine, Irvine, CA 92697, USA 4Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA (1)
1Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China 2Academy of Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China 3Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China (1)
ANZAC Research Institute, The University of Sydney (1)
Academia Sinica (1)
Academy Professor, Turku Centre for Biotechnology, University of Turku and Abo Akademi University, Turku, Finland (1)
Agronomy College/National Key Laboratory of Wheat and Corn Crop/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University ,Zhengzhou China (1)
Analytical Biochemistry and Proteomics Unit, IIBCE and Institut Pasteur de Montevideo (1)
Archaea Biology and Ecogenomics Unit, University of Vienna, Djerassiplatz 1, 1030 Wien (1)
BPMP, CNRS, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France (1)
Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Canada (1)
Bioinformatics Core, Weill Cornell Medicine-Qatar (1)
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht (1)
Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), Copenhagen, Denmark (1)
Brown University, Molecular Biology, Cell Biology, Biochemistry (1)
CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS-HKU Joint Laboratory of Metallomics on Health and Environment & CAS Center for Excellence in Nanoscience, Institute of High Energy Physics & National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing 100049, P. R. China (1)
CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics and National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing 100049, P. R. China (1)
CNCR,VU Amsterdam (1)
Cell Pathology Division 816F/ARC Children’s Hospital of Philadelphia The University of Pennsylvania 3615 Civic Center Blvd. 816F/ARC Philadelphia, PA 19104 Office: 267-426-2839 Fax: 267-426-5165 (1)
Center for Cell and Gene Therapy Department of Neurosurgery Baylor College of Medicine Houston, Texas, USA (1)
Center for Environmental and Human Toxicology Department of Physiological Sciences & College of Medicine College of Veterinary Medicine University of Florida (1)
Center for Proteomics & Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA (1)
Centre for Genomic Regulation, CRG (1)

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Mechanical force promotes dimethylarginine dimethylaminohydrolase 1-mediated hydrolysis of the metabolite asymmetric dimethylarginine to enhance bone formation

Mechanical force is critical for the development and remodeling of bone. Here we report that mechanical force regulates the production of the metabolite asymmetric dimethylarginine (ADMA) via regulating the hydrolytic enzyme dimethylarginine dimethylaminohydrolase 1 (Ddah1) expression in osteobla...

2021-11-23 | MTBLS3725 | MetaboLights

The nanoCUT&RUN technique visualizes telomeric chromatin in Drosophila.

Not available

S-EPMC9473618 | biostudies-literature

Mutational analysis of measles virus suggests constraints on antigenic variation of the glycoproteins

RNAseq of mutant measles virus libraries Insertional mutagenesis of measles to identify tolerated locations Mutant measles virus libraries were constructed as described in: Heaton, N.S., Sachs, D., Chen,C.J., Hai, R., and Palese, P. (2013). Genome-wide mutagenesis of influenza virus reveals un...

ORGANISM(S): Measles virus

2015-04-08 | E-GEOD-67666 | biostudies-arrayexpress

Targeted Intracellular Copper Reservoir Enhances Liver Cancer Immunotherapy.

Not available

S-EPMC12423925 | biostudies-literature

GNPS liver data files for liver data files for "Improved Annotation of Untargeted Metabolomics Data through Buffer Modifications That Shift Adduct Mass and Intensity"

This is the dataset associated with the following publication: Improved Annotation of Untargeted Metabolomics Data through Buffer Modifications That Shift Adduct Mass and Intensity. Wenyun Lu, Xi Xing, Lin Wang, Li Chen, Sisi Zhang, Melanie R McReynolds, Joshua D Rabinowitz. Anal Chem. 2020 Sep 1;9...

ORGANISM(S): Mus <mouse, Genus> (ncbitaxon:10088)

2021-03-30 | MSV000087131 | GNPS

Genome-wide map of R-loops reveals its interplay with transcription and genome integrity during germ cell meiosis.

Not available

S-EPMC10491972 | biostudies-literature

Expression profiling analysis of brain from ADAR2 mutant mice

ADARs, short for adenosine deaminases acting on RNA, were first found by their characteristic activity of deaminating up to 50% of all adenosines in double-stranded RNA in vitro. C. elegans has two ADARs, only one is found in the fly, and mammals express three ADARs. Importantly, the spectrum of phy...

ORGANISM(S): Mus musculus

2010-11-01 | E-GEOD-15383 | biostudies-arrayexpress

Imbalance of gut microbiota in gestational diabetes.

Not available

S-EPMC10983739 | biostudies-literature

Pla2g7 regulates bone homeostasis via Alox12/12-HETE/Gpr31 signaling axis

Bone homeostasis mainly depends on the equilibrium of osteoclasts and osteoblasts, overactivated osteoclasts play a pivotal role in the progression of osteoporosis. Here, we revealed that Pla2g7 (phospholipase A2 group VII) was positively correlated with bone resorption in clinic. By single-cell ...

2025-10-30 | MTBLS13141 | MetaboLights

The Estrogen Receptor Co-Regulator Protein, Proline Glutamic Acid and Leucine Rich Protein 1 (PELP1) Mediates Estrogen Rapid Signaling and Neuroprotection in the Brain

We examined the role of PELP1 in E2-ER-mediated transcription in the hippocampus under conditions of GCI by perfroming global transcriptome analysis. E2-treated FLOX and PELP1 FBKO mice were subjected to GCI followed by 24 h reperfusion and the isolated RNA was utilized for RNA-seq analysis. Our res...

ORGANISM(S): Mus musculus

2015-12-07 | E-GEOD-72136 | biostudies-arrayexpress

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946 Results

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