Rat model - OmicsDI

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Unknown (18282)
Transcriptomics (3264)
Genomics (2429)
Proteomics (541)
Metabolomics (113)
Models (44)
Methylation profiling (28)
Other (22)
Clinical (2)
Multiomics (1)

Organisms

Rattus norvegicus (1888)
Homo sapiens (698)
Mus musculus (621)
Rattus rattus (46)
Sus scrofa (26)
Arabidopsis thaliana (25)
Bos taurus (25)
Rattus (24)
Danio rerio (24)
Drosophila melanogaster (21)
Saccharomyces cerevisiae (20)
Caenorhabditis elegans (18)
Gallus gallus (18)
Zea mays (9)
Macaca mulatta (9)
Plasmodium falciparum (6)
Staphylococcus aureus (6)
Escherichia coli (6)
cellular organisms (5)
Colinus virginianus (5)
Carassius auratus (5)
Medicago truncatula (5)
Oryza sativa Japonica Group (5)
Canis lupus familiaris (5)
Bacillus subtilis subsp. subtilis str. 168 (4)
Bacillus subtilis (4)
Salmo salar (4)
Oncorhynchus mykiss (4)
Oryctolagus (1)
Mammalia (1)

Organisms

Rattus norvegicus (1274)
Homo sapiens (114)
Mus musculus (84)
rat gut metagenome (35)
Rattus (13)
Heterocephalus glaber (8)
rat metagenome (6)
gut metagenome (6)
Arvicanthis niloticus (5)
feces metagenome (5)
unidentified (5)
Rattus rattus (3)
Sus scrofa (2)
Escherichia coli (2)
mouse gut metagenome (2)
Didelphis virginiana (1)
Bacteroides fragilis 638R (1)
Grammomys surdaster (1)
Peromyscus maniculatus bairdii (1)
Streptococcus sanguinis SK36 (1)
Hirudo medicinalis (1)
Hippocampus (1)
Peromyscus polionotus (1)
Peromyscus californicus (1)
Psammomys obesus (1)
Cronobacter turicensis (1)
Peromyscus leucopus (1)
Nippostrongylus brasiliensis (1)
Leptospira interrogans serovar Manilae (1)
Streptococcus mutans UA159 (1)

Repository

ENA (2245)
biostudies-arrayexpress (2236)
geo (1262)
pride (336)
iProX (126)
MetaboLights (109)
MassIVE (40)
BioModels (34)
jPOST (20)
PMR (9)
PanoramaPublic (7)
PAXDB (6)
EGA (5)
ExpressionAtlas (4)
MetabolomicsWorkbench (3)
Cell Collective (1)
GNPS (1)
GPMDB (1)

Tissue

Brain (80)
Heart (37)
Cell culture (30)
Kidney (19)
Liver (19)
Lung (13)
Epithelial cell (11)
Blood plasma (9)
Primary cell (9)
Retina (9)
Hepatocyte (6)
Skin (6)
Blood cell (5)
Fibroblast (5)
Permanent cell line cell (5)
Spinal cord (5)
Stem cell (5)
B cell (4)
Blood serum (4)
Cardiac muscle cell (4)
Urine (4)
Blood (3)
Astrocyte (3)
Heart (1)
Brain (1)
Kidney (1)
Lung (1)
Spleen (1)
Liver (1)
Urine (1)

Disease

Normal (12)
Parkinson's disease (8)
Alzheimer's disease (6)
Botulism (2)
Diet induced obesity (1)
Lean control (1)
Cancer (1)
Pheocromocytoma cell line (1)
Pheochromocytoma (1)
Responder to preoperative radiotherapy (1)
Uninjured (1)
Cocaine addiction (1)
Model of metabolic syndrome (1)
Ischaemia reperfusion injury (1)
Hypertension (1)
Pneumococcal meningitis (1)
Subarachnoid hemorrhage NOS (1)
Insulin resistance (1)
Progressive skeletal muscle myopathy (1)
Photoreceptor degeneration (1)
Angiogenic chondrosarcoma (1)
Sham surgery (1)
Colon carcinoma (1)
SS2-infected (1)
Colon adenocarcinoma (1)
Tumor (1)
Cardiac hypertrophy (1)
Fibrosis (1)
Glioblastoma (1)
Insulin Resistance (1)

Technology Type

Mass Spectrometry (338)
Shotgun proteomics (197)
Bottom-up proteomics (63)
Mass spectrometry (61)
Mass spectrometry assay (35)
Data-dependent acquisition (29)
Data-independent acquisition (24)
Gel-based experiment (18)
SWATH MS (18)
Top-down proteomics (16)
NMR spectroscopy (14)
Affinity purification coupled with mass spectrometry proteomics (13)
HDMSE (7)
Chemical cross-linking coupled with mass spectrometry proteomics (3)
Proteogenomics (3)
ESI (2)
DiaPASEF (2)
Perlegen, Affymetrix, Illumina (1)
NMR (1)
Mass spectrometry imaging (1)
Metaproteomics (1)
SRM/MRM (1)

Instrument Platform

Illumina NovaSeq 6000 (36)
Illumina HiSeq 2500 (19)
NextSeq 500 (15)
Illumina HiSeq 4000 (14)
Illumina HiSeq 2000 (7)
Agilent High resolution C scanner (4)
Illumina HiSeq 1500 (4)
Illumina NovaSeq X (3)
NextSeq 2000 (3)
Illumina MiSeq (3)
NextSeq 550 (3)
Qubit 4.0 Fluorometer/ Agilen 5300 Fragment Analyzer (2)
Nanodrop 2000c spectrophotometer (1)
FastPrep-24 5G bead beater, Qubit Fluorometer (1)
12 well TC-treated plate, LETs buffer, dry ice (1)
10X Genomics Chromium v3.1 with multiplexing kit (1)
PromethION (1)
Computer and Applied Biosystems 7500 Real Time PCR Systems thermal cycler (1)
Illumina TruSeq (1)
Agilent 2100 Bioanalyzer, Applied Biosystems 7900HT Sequence Detection System, Illumina TruSeq Small RNA Sample Preparation Kit (1)
RNeasy mini Kit, Ribo-Zero Human/Mouse/Rat kit (1)
MoFlo XDP (Beckman Coulter) or a FACSAria II (Becton Dickinson) (1)
Fluidigm C1 autoprep system (1)
(Make:PerkinElmer,Model:ScanArray 4000XL) (1)
Agilent Bioanalyzer 2100 (1)
Agilent Microarray Scanner (1)
Agilent G2565BA scanner (1)
Agilent Hybridization Oven (1)
Agilent G2565BA Microarray Scanner System (Agilent Technologies) (1)
Tecan HS4800 hybridization station (Tecan) (1)

Publication Date

2010 (345)
2015 (339)
2013 (335)
2014 (304)
2026 (281)
2012 (256)
2025 (253)
2011 (212)
2024 (210)
2016 (206)
2022 (199)
2021 (176)
2023 (175)
2008 (172)
2009 (160)
2020 (130)
2007 (95)
2018 (84)
2017 (81)
2019 (79)
2005 (37)
2006 (31)
2004 (13)
2003 (3)

UNIPROT ID/AC

P63086 (3)
Q01986 (3)
Q62636 (2)
Q9QYV3 (2)
P47196 (2)
P47197 (2)
P21708 (2)
P36506 (2)
Q99MC6 (2)
P11345 (2)
P50904 (2)
Q9Z1I2 (2)
Q63531 (2)
Q9Z1I1 (2)
Q63484 (2)
Q9QX70 (2)
P07522 (2)
P06238 (1)
P20961 (1)
Q71SA3 (1)
P17246 (1)
P29598 (1)
Q01177 (1)
F1LV89 (1)
F1M9C3 (1)
Q63787 (1)
P04150 (1)
P08235 (1)
Q12778 (1)
Q9UBK2 (1)

ENSEMBL ID

ENSRNOG00000000558.4 (1)
ENSRNOG00000001492.4 (1)
ENSRNOG00000029871.2 (1)
ENSRNOG00000008479.4 (1)
ENSRNOG00000012794.4 (1)
ENSRNOG00000029938.2 (1)
ENSRNOG00000032085.2 (1)
ENSRNOG00000013971.4 (1)
ENSRNOG00000019490.4 (1)
ENSRNOG00000018567.4 (1)
ENSRNOG00000016356.4 (1)
ENSRNOG00000021265.3 (1)
ENSRNOG00000020361.4 (1)
ENSRNOG00000037948.1 (1)
ENSRNOG00000005981.4 (1)
ENSRNOG00000003069.2 (1)
ENSRNOG00000010539.3 (1)
ENSRNOG00000030636.2 (1)
ENSRNOG00000020110.3 (1)
ENSRNOG00000020606.4 (1)
ENSRNOG00000018267.4 (1)
ENSRNOG00000008544.2 (1)
ENSRNOG00000003253.3 (1)
ENSRNOG00000038085.1 (1)
ENSRNOG00000029207.2 (1)
ENSRNOG00000013436.3 (1)
ENSRNOG00000010280.4 (1)
ENSRNOG00000019005.3 (1)
ENSRNOG00000006979.4 (1)
ENSRNOG00000020828.4 (1)

CHEBI ID

CHEBI:16919 (31)
CHEBI:18237 (22)
CHEBI:16027 (20)
CHEBI:17234 (19)
CHEBI:17126 (13)
CHEBI:16761 (12)
CHEBI:16238 (10)
CHEBI:17287 (9)
CHEBI:15846 (8)
CHEBI:15351 (3)
CHEBI:15422 (3)
CHEBI:16908 (3)
CHEBI:30788 (2)
CHEBI:61902 (2)
CHEBI:27803 (2)
CHEBI:17387 (2)
CHEBI:37554 (2)
CHEBI:13389 (2)
CHEBI:15531 (2)
CHEBI:15525 (2)
CHEBI:15346 (2)
CHEBI:24996 (2)
CHEBI:17138 (2)
CHEBI:15361 (2)
CHEBI:16526 (2)
CHEBI:50211 (1)
CHEBI:3892 (1)
CHEBI:65311 (1)
CHEBI:25212 (1)
CHEBI:89363 (1)

Metabolite Name

Uracil (29)
Creatinine (29)
Creatine (28)
Hypoxanthine (27)
Inosine (26)
Taurine (25)
Uridine (24)
Pantothenic acid (21)
Choline (21)
Cholic acid (21)
Cytosine (20)
Indole (18)
Xanthosine (18)
Xanthine (18)
Thymine (17)
Niacinamide (17)
Citrulline (17)
L-Proline (17)
Allantoin (17)
Taurocholic acid (17)
Deoxycholic acid (17)
Riboflavin (17)
L-Glutamine (17)
Uric acid (17)
L-Isoleucine (17)
Hippuric acid (17)
Betaine (16)
Kynurenic acid (16)
Ornithine (16)
Citric acid (16)

First Public Date

2026 (367)
2014 (313)
2024 (271)
2025 (270)
2023 (221)
2022 (155)
2021 (150)
2020 (133)
2019 (87)
2017 (83)
2018 (69)
2015 (58)
2016 (40)
2013 (26)
2012 (1)
2010 (1)

Modelling Approach

Ordinary differential equation model (28)
Physiologically based pharmacokinetic model (2)
Constraint-based model (2)
Computational model (1)

Study status

Recruiting (2)

Lab affiliation

Helmholtz-Centre for Environmental Research - UFZ (4)
Aarhus University Hospital, Denmark (3)
Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, USA (3)
1The Rappaport Faculty of Medicine and Research Institute, Haifa 3109601, Israel; 2Network Biology Research Laboratories, Technion-Israel Institute of Technology, Haifa 3200003, Israel (2)
Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana 47907, United States (2)
Core Facility for Mass Spectrometry and Proteomics, Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany (2)
Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark. (2)
Department of Chemistry, Johns Hopkins University, Baltimore, Maryland, United States (2)
Department of Glycobiology, Institute of Chemistry, Slovak Academy of Sciences (2)
Department of Molecular Biology and Endocrinology, “VINČA”, Institute of Nuclear Sciences - National Institute of thе Republic of Serbia, University of Belgrade, Belgrade, Serbia (2)
Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi-221005, India (2)
Departments of Biochemistry and Neurology Emory University School of Medicine (2)
Div. Clinical Protein Science & Imaging, Dept. of Clinical Sciences (Lund) and Dept. of Biomedical Engineering, Lund University, Lund, Sweden (2)
Foetal Exposure Group School of Clinical Sciences University of Bristol United Kingdom (2)
Head of the Curie Institute Mass Spectrometry Platform (2)
Institute of Bioorganic Chemistry Polish Academy of Sciences (2)
Instituto de Investigaciones Sanitarias de Santiago de Compostela (2)
Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 NeuchÃƒÂ¢tel, Switzerland (part of Philip Morris International group of companies) (2)
Philip Morris R&D, Neuchatel, Switzerland (2)
Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Sweden (2)
Proteomics Core Facility, University of Gothenburg (2)
School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison (2)
Shandong university of Traditional Chinese Medicine (2)
Systems Biology Ireland, University College Dublin (2)
Texas Tech University (2)
1) Department Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany; 2) Institute for Bioanalysis, University of Applied Science Coburg, Coburg, Germany (1)
1) Department of Analytical Chemistry and Biochemistry, AGH University of Krakow, Krakow, Poland 2) Laboratory of Proteomics and Mass Spectrometry, Maj Institute of Pharmacology, Polish Academy of Sciences, Krakow, Poland (1)
1) Department of Analytical Chemistry and Biochemisty, AGH University of Krakow 2) Laboratory of Proteomics and Mass Spectrometry, Maj Institute of Pharmacology, Polish Academy of Sciences (1)
Aalborg University Fredrik Bajersvej 3B 9220 Aalborg (1)
Aarhus University Department of Biomedicine Høegh-Guldbergsgade 10 DK-8000 Aarhus C (1)

Keyword

Postoperative insulin resistance (1)
Branched chain amino acids (1)
Cetuximab (1)

IsPrivate

False (34)

Model Flag

Non Miriam (2)
Non Kinetic (1)

Submitter Keywords

Ersilia (1)
FAIR-AIML (1)
Machine Learning Model (1)
TransQST (1)
FROG (1)

Classification

bacteria (11)
fungi (1)
viruses (1)
protozoa (1)

Modification

0.984 (1)
15.99491 (1)
15.994915 (1)
1x(15)N labeled L-valine (1)
4-tetrahydrothiazine-3-carboxylic acid (1)
57.02146 (1)
57.021464 (1)
6x(2)H labeled dimethylated L-arginine (1)
Not available (1)

Study type

Transcription profiling by array (1650)
RNA-seq of coding RNA (263)
Unknown experiment type (68)
ChIP-seq (31)
RNA-seq of non coding RNA (31)
Comparative genomic hybridization by array (23)
Other (20)
Methylation profiling by array (18)
ChIP-chip by tiling array (14)
RNA-seq of coding RNA from single cells (14)
Transcription profiling by RT-PCR (12)
Methylation profiling by high throughput sequencing (10)
Animal - High-throughput sequencing (9)
Transcription profiling by SAGE (8)
Animal - One-color microarray (8)
RNA-seq of total RNA (7)
Transcription profiling by tiling array (6)
ChIP-chip by array (6)
Proteomic profiling by array (6)
Genotyping by array (5)
MicroRNA profiling by high throughput sequencing (4)
Animal - Single-cell sequencing (2)
High-throughput sequencing (2)
MicroRNA profiling by array (2)
DNA-seq (2)
Transcription profiling by MPSS (1)
RIP-chip by array (1)
Cell line - One-color microarray (1)
Translation profiling (1)
Human - One-color microarray (1)

Release Date

2022 (2152)
2025 (1934)
2021 (1909)
2023 (1811)
2020 (1600)
2024 (1526)
2019 (1178)
2018 (1106)
2017 (981)
2015 (976)
2016 (909)
2014 (841)
2013 (699)
2012 (542)
2010 (539)
2011 (483)
2009 (311)
2008 (305)
2026 (268)
2007 (150)
2006 (71)
2005 (66)
2004 (46)
2003 (26)
2002 (22)
2000 (21)
1999 (16)
1998 (11)
2001 (10)
1997 (5)

Location

China (1)
Italy (1)

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Tissue, urine and serum NMR metabolomics dataset from a 5/6 nephrectomy rat model of chronic kidney disease

Serum, urine and tissue from a rat model of chronic kidney disease (CKD) were analysed using nuclear magnetic resonance (NMR) spectroscopy-based metabolomics methods, and compared with samples from sham operated rats. Both urine and serum were sampled at multiple timepoints, and the results have ...

2020-11-16 | MTBLS2052 | MetaboLights

Serum Metabolomics in the Rat Model of Recurrent Pelvic Pain

This study aimed to investigate systemic metabolic alterations underlying pain-depression comorbidity in the Recurrent Pelvic Pain (RPP) rat model using untargeted serum metabolomics (UPLC-Q-Orbitrap-MS). Comparative analysis revealed distinct metabolic profiles, identifying 234 differential meta...

2026-02-11 | MTBLS13869 | MetaboLights

Untargeted metabolomics profiling of esophageal tissues from a rat model of reflux esophagitis treated with Shunwei Jiangni Decoction

This dataset contains raw untargeted metabolomics data generated from esophageal tissue samples of rats in a reflux esophagitis (RE) model. The study aimed to characterize metabolic alterations associated with RE pathogenesis and to evaluate the regulatory effects of Shunwei Jiangni Decoction (SW...

2026-04-10 | MTBLS14112 | MetaboLights

Rat serum transcriptomic data

study investigated the anti-fatigue effect of the Panax ginseng–Astragali Radix (GGJ) herb pair, the core functional unit of Baoyuan Decoction, using a rat fatigue model induced by forced swimming. Serum samples were collected for untargeted metabolomics analysis by LC-MS/MS to profile differenti...

2026-06-30 | MTBLS14902 | MetaboLights

Therapeutic Effect of Buyang Huanwu Decoction on the Gut Microbiota and Hippocampal Metabolism in a Rat Model of Cerebral Ischemia

Buyang Huanwu decoction (BHD) is a well-known Chinese herbal prescription. It has been widely used in the clinical treatment of cerebral ischemia (CI) in China. However, the mechanism underlying the treatment of CI with BHD remains to be elucidated. In this study, we combined microbiomic and meta...

2022-06-02 | MTBLS4366 | MetaboLights

Therapeutic effects of traditional Chinese medicine compound Hua-Feng-Dan in a rat model of ischemic stroke involve renormalization of gut microbiota

Hua-Feng-Dan is a traditional Chinese medicine compound used to treat ischemic stroke, but little is known about its therapeutic mechanism. This study explored whether and how the mechanism involves readjustment of gut microbiota. Rats were subjected to middle cerebral artery occlusion as a model...

2025-01-06 | MTBLS10818 | MetaboLights

Untargeted metabolomics of offspring rats in MIA model

Maternal immune activation is a significant environmental factor for neurodevelopmental diseases. Although gut bacteria and their metabolites are linked to behavioral deficits in NDDs, the roles of gut fungi and secondary fungal metabolites remain unclear. Here, we induced MIA via a single intrap...

2026-01-20 | MTBLS12687 | MetaboLights

Untargeted gas chromatography–mass spectrometry-based metabolomics analysis of kidney and liver tissue from the Lewis Polycystic Kidney rat

Polycystic kidney disease (PKD) encompasses a spectrum of inherited disorders that lead to end-stage renal disease (ESRD). There is no cure for PKD and current treatment options are limited to renal replacement therapy and transplantation. A better understanding of the pathobiology of PKD is needed ...

2023-01-26 | MTBLS748 | MetaboLights

Efficacy of Zhuyu Pill Intervention in a Cholestasis Rat Model: Mutual Effects on Fecal Metabolism and Microbial Diversity

Cholestasis is a clinical condition resulting from the impairment of bile flow. Currently, patients with cholestasis still face several barriers in seeking diagnosis and treatment. Zhuyu Pill (ZYP) is an ancient classic formula of the Coptis-Evodia herb couples (CEHC), and has been used for chole...

2022-05-30 | MTBLS2721 | MetaboLights

NAD(P) deficiency plays an important role in the restraint-stress-induced depression in the rat model

Not available

ORGANISM(S): Rattus norvegicus

ST002298 | MetabolomicsWorkbench

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