Shen Min M - OmicsDI

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Unknown (301)
Proteomics (295)
Metabolomics (108)
Transcriptomics (76)
Genomics (25)

Organisms

Schizosaccharomyces pombe (282)
Sinorhizobium meliloti BL225C (282)
Sus scrofa domesticus (282)
Saccharomyces cerevisiae (282)
Staphylococcus aureus (282)
Rattus norvegicus (282)
Escherichia coli (282)
Methylohalobius crimeensis 10Ki (282)
Homo sapiens (49)
Mus musculus (29)
Campylobacter jejuni (5)
Saccharomyces cerevisiae (5)
Sus scrofa (3)
Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 (2)
Xerophyta humilis (2)
Caenorhabditis elegans (2)
Rattus norvegicus (2)
Arabidopsis thaliana (2)
Rattus rattus (2)
unidentified microorganism (1)
Capra hircus (1)
uncultured bacterium (1)
Gossypium hirsutum (1)
Theobroma cacao (1)
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Ovis aries (1)
Oryza sativa Japonica Group (1)
Triticum aestivum (1)
Drosophila melanogaster (1)
Severe acute respiratory syndrome coronavirus 2 (1)

Organisms

Mus musculus (1)

Repository

pride (282)
MetaboLights (108)
biostudies-arrayexpress (100)
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EGA (2)
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ENA (1)

Tissue

Cell culture (54)
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Thyroid nodule (2)
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Disease

Breast cancer (5)
Disease free (5)
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Malignant neoplasm of ovary (3)
Non-alcoholic steatohepatitis (2)
Ovarian cancer (2)
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Influenza (2)
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Amyloidosis (1)
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Polycystic kidney disease (1)
Antenatal onset (1)
Hydronephrosis (1)
Synovial sarcoma (1)
Nephrotic syndrome (1)
Fungal infectious disease (1)
Thyroid cancer (1)
Intestinal schistosomiasis (1)
Inflammation (1)
Toxoplasmosis (1)
Stomach cancer (1)
Skin melanoma (1)

Technology Type

Mass Spectrometry (282)
Shotgun proteomics (154)
Mass spectrometry (83)
Bottom-up proteomics (48)
Data-dependent acquisition (27)
Mass spectrometry assay (22)
Affinity purification coupled with mass spectrometry proteomics (22)
Gel-based experiment (17)
Top-down proteomics (16)
Data-independent acquisition (14)
SWATH MS (8)
SRM/MRM (6)
Chemical cross-linking coupled with mass spectrometry proteomics (4)
NMR spectroscopy (3)
DiaPASEF (3)
Metaproteomics (2)
Proteogenomics (2)
Immunopeptidomics (2)
All-ion fragmentation (2)
Glycoproteomics (1)
Affinity proteomics (1)

Instrument Platform

Liquid Chromatography MS - positive - reverse phase (47)
Liquid Chromatography MS - negative - reverse phase (33)
Liquid Chromatography MS - negative - hilic (18)
Liquid Chromatography MS - positive - hilic (18)
Illumina NovaSeq 6000 (9)
HiSeq X Ten (6)
Illumina HiSeq 2000 (5)
NextSeq 500 (4)
Liquid Chromatography MS - alternating - reverse-phase (4)
Liquid Chromatography MS - positive - reverse-phase (4)
Liquid Chromatography MS - negative - reverse-phase (4)
Liquid Chromatography MS - (3)
Liquid Chromatography MS - positive (3)
Gas Chromatography MS - positive (2)
6540 Q-TOF LC/MS (Agilent) (2)
Nuclear Magnetic Resonance (NMR) - (2)
Liquid Chromatography MS - negative (2)
Liquid Chromatography MS - alternating - reverse phase (2)
Illumina HiSeq 2000 platform (1)
Affymetrix GeneChip Scanner 3000 7G (1)
Illumina Genome Analyzer II (1)
NextSeq 550 (1)
Illumina HiSeq 2500 (1)
Orbitrap Fusion (1)
Agilent 7890A GC-LECO Pegasus HT TOFMS (1)
Liquid Chromatography MS - negative - HILIC - Triple 6600 (AB Sciex) (1)
Liquid Chromatography MS - negative - HILIC - TripleTOF 6600 (AB Sciex) (1)
Liquid Chromatography MS - Negative (LC-MS (NEG)) (1)
Liquid Chromatography MS - Positive (LC-MS (POS)) (1)
Liquid Chromatography MS -neg - hilic (1)

Publication Date

2022 (69)
2025 (61)
2026 (54)
2021 (54)
2023 (43)
2024 (41)
2018 (25)
2020 (24)
2019 (24)
2013 (21)
2016 (17)
2014 (15)
2015 (13)
2017 (8)
2012 (7)
2010 (5)
2011 (4)
2008 (3)
2009 (2)
2007 (2)
2005 (2)
2006 (1)
2027 (1)

CHEBI ID

CHEBI:16704 (30)
CHEBI:17368 (30)
CHEBI:16335 (28)
CHEBI:17568 (28)
CHEBI:17295 (28)
CHEBI:30769 (28)
CHEBI:16708 (27)
CHEBI:17015 (27)
CHEBI:17895 (27)
CHEBI:17154 (26)
CHEBI:16015 (26)
CHEBI:16750 (25)
CHEBI:17750 (25)
CHEBI:16919 (25)
CHEBI:17596 (25)
CHEBI:15756 (25)
CHEBI:17351 (25)
CHEBI:17203 (24)
CHEBI:15891 (24)
CHEBI:16828 (24)
CHEBI:18344 (24)
CHEBI:16040 (23)
CHEBI:16467 (23)
CHEBI:55328 (23)
CHEBI:16359 (23)
CHEBI:17562 (22)
CHEBI:17509 (22)
CHEBI:7916 (22)
CHEBI:15971 (22)
CHEBI:16027 (22)

Metabolite Name

Hypoxanthine (28)
Adenine (27)
Creatine (25)
Taurine (24)
Adenosine (24)
Creatinine (24)
Guanosine (23)
Uridine (23)
Uracil (22)
Inosine (22)
Betaine (21)
Riboflavin (21)
L-Phenylalanine (21)
L-Arginine (20)
L-Histidine (20)
Cytidine (20)
L-Tyrosine (20)
Nicotinamide (18)
Choline (18)
Cholic acid (17)
Oleamide (17)
Cytosine (17)
4-Pyridoxic acid (16)
L-Tryptophan (16)
L-Glutamine (16)
Sucrose (16)
L-Carnitine (16)
Glycine (15)
L-Proline (15)
Kynurenic acid (15)

First Public Date

2018 (1)

Modification

2x(15)N labeled L-lysine (1)
4x(15)N labeled L-arginine (1)

Study type

Transcription profiling by array (33)
ChIP-seq (16)
RNA-seq of coding RNA (11)
Methylation profiling by high throughput sequencing (6)
ChIP-chip by tiling array (3)
Animal - High-throughput sequencing (3)
4C (3)
ATAC-seq (3)
Other (3)
Transcription profiling by RT-PCR (2)
Comparative genomic hybridization by array (2)
Proteomic profiling by array (2)
RNA-seq of non coding RNA (2)
Unknown experiment type (1)
Human - High-throughput sequencing (1)
High-throughput sequencing (1)
Cell line - High-throughput sequencing (1)
Transcription profiling by tiling array (1)
ChIP-chip by array (1)
Capture-C (1)
MicroRNA profiling by array (1)
Methylation profiling by array (1)
CUT&RUN (1)
RNA-seq of total RNA (1)

Release Date

2025 (49)
2023 (40)
2021 (40)
2022 (36)
2024 (30)
2013 (27)
2014 (24)
2020 (21)
2019 (17)
2016 (16)
2017 (16)
2015 (15)
2012 (13)
2010 (13)
2018 (13)
2026 (10)
2011 (9)
2009 (3)
2008 (3)
2007 (3)
2005 (2)
2006 (1)

Lab affiliation

Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA. Systems Biology Institute, Yale University, New Haven, CT 06516, USA (7)
West China Second University Hospital, Sichuan University (4)
Michigan State University (4)
University at buffalo, SUNY (3)
Department of Biology, University of Rochester, NY, USA (3)
SIMM (3)
Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA. Systems Biology Institute, Yale University, New Haven, CT 06516, USA (3)
Department of Chemistry, Michigan State University (3)
Fudan University (3)
State Key Laboratory of Reproductive Medicine, Nanjing Medical University (3)
Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697, USA (2)
yangjinguang@caas.cn (2)
Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM) (2)
Jiangsu Academy of Agricultural Sciences (2)
Brigham Young University (2)
Institut für Mikrobiologie, Universität Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald (2)
the First Affiliated Hospital of Chongqing Medical University (2)
Abbvie Bioresearch Center (2)
Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China (2)
Translational Genomics Research Institute (2)
State Key Laboratory of Reproductive Medicine and Offspring Health， Nanjing Medical University, Nanjing, China. (2)
Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China (2)
Sun yat-sen university cancer center (2)
Hubei University of Medicine, Taihe Hospital (2)
Keck MS & Proteomics Resource Yale School of Medicine (2)
Shanghai Institute of Materia Medica (2)
Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, USA (2)
Department of Nephrology, Children's Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China. (1)
Molecular Biology and Lewis-Sigler Institute for Intergrative Genomics, Princeton University, USA (1)
Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, USA (1)

Tags

xref:PubMed:23747202 (1)
xref:PubMed:30457566 (1)
xref:PubMed:32055844 (1)
xref:PubMed:34412677 (1)
xref:PubMed:31903125 (1)

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DNA Cytosine Hydroxymethylation Levels Are Distinct Among Peripheral Blood Leukocytes

Peripheral blood leukocytes are the most commonly used surrogates to study epigenome-induced risk and epigenomic response to disease related stress. We considered the hypothesis that the TET enzyme catalyzed hydroxymethylation of 5mC to 5hmC might vary among peripheral blood leukocytes and reflect t...

ORGANISM(S): Homo sapiens

2016-07-05 | E-GEOD-70519 | biostudies-arrayexpress

ATRX tolerates activity-dependent histone H3 M-bM-^@M-^\methyl/phos switchingM-bM-^@M-^] to maintain repetitive element silencing in neurons

ATRX is a member of the SWI2/SNF2 family of chromatin remodeling proteins and primarily functions at heterochromatic loci via its recognition of M-bM-^@M-^XrepressiveM-bM-^@M-^Y histone modifications (e.g., H3K9me3). Despite significant roles for ATRX during normal neural development, as well as its...

ORGANISM(S): Mus musculus

2015-01-02 | E-GEOD-64062 | biostudies-arrayexpress

Subsets of visceral adipose tissue nuclei with discrete levels of 5-hydroxymethylcytosine

We explored the hypothesis that adipose tissue contains epigenetically distinct subpopulations of adipocytes that are differentially potentiated to record cellular memories of their environment. Adipocytes are large, fragile, and technically difficult to efficiently isolate and fractionate. We devel...

ORGANISM(S): Sus scrofa

2016-07-20 | E-GEOD-73684 | biostudies-arrayexpress

Single-cell RNA sequencing reveals Shen-Bai-Jie-Du decoction retards colorectal tumorigenesis by regulating the TMEM131-TNF signaling pathway-mediated differentiation of immunosuppressive dendritic cells.

Not available

S-EPMC12278398 | biostudies-literature

Proteomics on proteins from freshwater anaerobic methanotrophs that forms cytochrome nanowires

Anaerobic methanotrophic archaea are key components of the biological methane filter, but progress in understanding their physiology has been limited by the lack of axenic cultures. This study establishes near-axenic electrode-grown cultures of a freshwater anaerobic methanotroph, proposed as Candid...

ORGANISM(S): Candidatus Methanoperedens

2026-08-28 | PXD072602 | Pride

ERK activation drives intestinal tumorigenesis in Apc(min/+) mice.

Not available

S-EPMC2882530 | biostudies-literature

Seroprevalence and evolutionary dynamics of genotype 4 hepatitis E virus in Shandong Province, China.

Not available

S-EPMC4069323 | biostudies-literature

A novel dual histone mark reader ZCWPW2 regulates meiotic recombination through lactylation and transcriptional control in humans and mice

Meiotic recombination ensures proper chromosome segregation and genetic diversity during gametogenesis, and its disruption leads to infertility. It is known that the dual histone methylation writer–reader system, in which PRDM9 deposits H3K4me3 and H3K36me3 marks at nucleosomes to specify recombinat...

ORGANISM(S): Homo sapiens (Human)

2026-01-07 | PXD070427 | Pride

Meiotic recombination zcwpw1–zcwpw2 complex prdm9/zcwpw1/zcwpw2 system ldha ep300 lactylation

A novel dual histone mark reader ZCWPW2 regulates meiotic recombination through lactylation and transcriptional control in humans and mice

ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse)

2026-01-07 | PXD068838 | Pride

Meiotic recombination zcwpw1–zcwpw2 complex prdm9/zcwpw1/zcwpw2 system ldha ep300 lactylation

Phosphoproteomics of Jatropha curcas seedling under chilling stress

As a promising energy plant for biodiesel, Jatropha curcas is a tropical and subtropical shrub. Chilling is a major abiotic stress affecting the growth and development of J. curcas. In this study, we adopt the phosphoproteomic analysis, physiological measurement, ultrastructure observation to illust...

ORGANISM(S): Jatropha curcas

2019-01-09 | PXD011438 | Pride

Jatropha curcas phosphoproteomics seedling chilling stress regulated mechanism

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