Mouse brain cortex

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Unknown (3864)
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Organisms

Mus musculus (1223)
Schizosaccharomyces pombe (295)
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mixed sample (3)
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synthetic construct (1)
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Mus (1)

Organisms

Mus musculus (818)
Homo sapiens (56)
Rattus norvegicus (6)
Callithrix jacchus (3)
Macaca mulatta (3)
Mus musculus musculus (2)
Scotinomys teguina (1)
Tupaia belangeri chinensis (1)
mouse brain metagenome (1)
Lyssavirus rabies (1)
unidentified (1)
Danio rerio (1)
Eukaryota (1)
Drosophila melanogaster (1)
gut metagenome (1)
mouse gut metagenome (1)

Repository

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biostudies-arrayexpress (772)
geo (574)
pride (295)
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EVA (1)
GPMDB (1)
PAXDB (1)
PeptideAtlas (1)

Tissue

Brain (260)
Cerebral cortex (15)
Cell culture (15)
Astrocyte of the cerebral cortex (8)
Hippocampus (6)
Neuron of cerebral cortex (6)
Cerebral cortex neuron (6)
Neuron (5)
Microglial cell (4)
Cerebrospinal fluid (4)
Blood plasma (4)
Cerebellum (3)
Cortex (3)
Brain (3)
Frontal cortex (3)
CNS neuron (sensu Vertebrata) (3)
Primary neuron (3)
Tissue (3)
Hippocampal neuron (3)
Liver (3)
Hippocampus (hippocampal formation) (2)
Astroglial cell (2)
Regional part of brain (2)
Neuron cellular homeostasis (2)
Synapse (2)
Frontal lobe (2)
Brain cortex (1)
Striatum (1)
Preoptic area (1)
Medial prefrontal cortex (1)

Disease

Alzheimer's disease (21)
Huntington Disease (9)
Autism spectrum disorder (7)
Parkinson's disease (7)
Disease free (7)
Amyotrophic lateral sclerosis (4)
Normal (3)
Multiple sclerosis (3)
Cerebral ischemia (2)
Major depressive disorder (2)
Frontotemporal dementia (2)
Fragile X syndrome (2)
Brain cancer (2)
Schizophrenia (2)
Wounds and Injuries (2)
HIV encephalitis (1)
Rett syndrome (1)
Temporal lobe epilepsy (1)
Reference (1)
Not Available (1)
Amyotrophic lateral sclerosis type 6 (1)
TANGO2-related metabolic encephalopathy and arrythmias (1)
Subcortical band heterotopia (1)
Carotid artery occlusion (1)
Cognitive impairment (1)
Leukoencephalopathy with vanishing white matter (1)
Autistic disorder (1)
Tauopathy (1)
Krabbe disease (1)
Epilepsy with generalized tonic-clonic seizures (1)

Technology Type

Mass Spectrometry (297)
Shotgun proteomics (149)
Bottom-up proteomics (76)
Data-dependent acquisition (39)
Data-independent acquisition (25)
Affinity purification coupled with mass spectrometry proteomics (21)
Mass spectrometry (16)
Mass spectrometry assay (14)
Gel-based experiment (13)
SWATH MS (12)
Top-down proteomics (9)
HDMSE (5)
All-ion fragmentation (3)
SRM/MRM (3)
EI (2)
ESI (2)
Mass spectrometry imaging (2)
PAcIFIC (1)
Proteogenomics (1)
Affinity proteomics (1)
MSE (1)
DiaPASEF (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (21)
Illumina HiSeq 2500 (18)
Orbitrap Fusion Lumos (13)
NextSeq 500 (10)
Q Exactive HF (7)
Illumina HiSeq 4000 (6)
Illumina HiSeq 2000 (4)
NextSeq 2000 (3)
Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis. (2)
Illumina NovaSeq X (2)
HiSeq X Ten (2)
NextSeq 550 (2)
6550 iFunnel Q-TOF LC/MS (2)
Chromium Next GEM Chip G (1)
10X v3 (1)
Qubit 4.0 and TapeStation (1)
Element AVITI (1)
Illumina® (NEB, USA) (1)
MouseWG-6_V2_0_R3_11278593_A (1)
Ion Chef™ System and Ion S5™ System or Ion GeneStudio™ S5 Systems. (1)
Not applicable (1)
Illumina Genome Analyzer IIx (1)
GenePix 4000B [Axon Instruments] (1)
Scanning hardware (1)
Illumina MiniSeq (1)
N/a (1)
MinION (1)
Ion Torrent S5 XL (1)
- (1)
Instrument (1)

Publication Date

2025 (156)
2026 (146)
2015 (128)
2013 (126)
2024 (111)
2023 (111)
2014 (97)
2016 (96)
2022 (94)
2021 (91)
2011 (80)
2012 (76)
2019 (68)
2020 (65)
2010 (64)
2018 (55)
2008 (55)
2017 (43)
2009 (37)
2007 (25)
2006 (12)
2005 (11)
2003 (5)

UNIPROT ID/AC

CAD10_MOUSE (1)
KCNA2_MOUSE (1)
DLGP2_MOUSE (1)
PPR29_MOUSE (1)
CP46A_MOUSE (1)
GBRA3_MOUSE (1)
K1549_MOUSE (1)
CLD11_MOUSE (1)
HCN1_MOUSE (1)
KCIP4_MOUSE (1)
GRIA1_MOUSE (1)
TSN2_MOUSE (1)
ST32C_MOUSE (1)
GD1L1_MOUSE (1)
ATCAY_MOUSE (1)
DGKB_MOUSE (1)
GABR1_MOUSE (1)
SC6A1_MOUSE (1)
CTND2_MOUSE (1)
NEGR1_MOUSE (1)
HECAM_MOUSE (1)
SHAN2_MOUSE (1)
F169A_MOUSE (1)
RB39B_MOUSE (1)
GRIA3_MOUSE (1)
ASTN1_MOUSE (1)
CNTP2_MOUSE (1)
UN13A_MOUSE (1)
NFASC_MOUSE (1)
BRSK2_MOUSE (1)

ENSEMBL ID

ENSG00000147251 (1)
ENSG00000229353 (1)
ENSG00000170477 (1)

CHEBI ID

CHEBI:16737 (5)
CHEBI:27515 (1)
CHEBI:6801 (1)
CHEBI:7274 (1)
CHEBI:27491 (1)
CHEBI:16675 (1)
CHEBI:28058 (1)
CHEBI:34665 (1)
CHEBI:28175 (1)
CHEBI:18163 (1)
CHEBI:17364 (1)
CHEBI:17431 (1)
CHEBI:27910 (1)
CHEBI:17737 (1)
CHEBI:17123 (1)
CHEBI:16797 (1)
CHEBI:16082 (1)
CHEBI:16290 (1)
CHEBI:1670 (1)
CHEBI:28541 (1)
CHEBI:30794 (1)
CHEBI:28888 (1)
CHEBI:44074 (1)
CHEBI:48714 (1)
CHEBI:28453 (1)
CHEBI:17425 (1)
CHEBI:16978 (1)
CHEBI:17173 (1)
CHEBI:16313 (1)
CHEBI:52595 (1)

Metabolite Name

Hypoxanthine (7)
Uracil (6)
Inosine (6)
Uridine (6)
Catechin (5)
Deoxycholic acid (5)
Arachidonic acid (5)
Glyceric acid (5)
Citrulline (5)
Taurine (5)
Cytidine (5)
Xanthine (5)
Guanosine (5)
Adenylsuccinic acid (4)
Valine (4)
Ouabain (4)
Leucine (4)
Betaine (4)
S-Adenosylhomocysteine (4)
Carnosine (4)
Mupirocin (4)
Maleic acid (4)
Allantoin (4)
1-Methylhistidine (4)
Pantothenic acid (4)
Citric acid (4)
Pipecolic acid (4)
Urocanic acid (4)
Spermidine (4)
Myo-Inositol (4)

First Public Date

2025 (161)
2026 (134)
2024 (121)
2023 (120)
2021 (91)
2014 (88)
2022 (68)
2019 (65)
2020 (59)
2017 (48)
2018 (41)
2015 (31)
2016 (19)
2013 (18)
2011 (2)

Lab affiliation

Research Unit for Molecular Medicine, Department of clinical Medicine, Aarhus University, Aarhus, Denmark (5)
Key Laboratory of Brain Functional Genomics of Shanghai and Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, China (3)
Institute of Genetics & Developmental Biology, Chinese Academy of Sciences (2)
Central South University (2)
Department of Neuro- and Sensory Physiology University Medical Center Göttingen Humboldtallee 23 37073 Göttingen (2)
Research Unit Protein Science, Helmholtz Zentrum München (2)
Neurologische Klinik und Poliklinik des Universitätsklinikums Neurology Josef-Schneider-Straße 11 97080 Würzburg Germany (2)
Institute of Clinical Pharmacology, Goethe-University, Frankfurt am Main, Germany (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)
Department of Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA (2)
Dept Biomedical Sciences, School of Medicine and Health Sciences, Institute of Neurosciences, Universitat de Barcelona, E-08036 Barcelona (2)
Department of Translational Research in Psychiatry Max Planck Institute of Psychiatry, Munich (2)
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, United States (2)
Hubei University of Medicine, Taihe Hospital (2)
Keck MS & Proteomics Resource Yale School of Medicine (2)
IRCCS Istituto G Gaslini (2)
Head of the Curie Institute Mass Spectrometry Platform (2)
Macquarie Medical School Macquarie University Australia Sydney 2109 (1)
Research Center, The Second Affiliated Hospital of Dalian Medical University, Dalian, China (1)
State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau 999078 (1)
Max Delbrück Center for Molecular Medicine in the Helmholtz association (MDC) Robert-Rössle-Straße 10 13125 Berlin (1)
Queensland Brain Institute, Bredy Lab, University of Queensland, Australia (1)
Department of Neuroscience , Tufts University (1)
Traumatic Brain Injury Research, Roskamp Institute, Sarasota, FL, USA (1)
Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China. (1)
Roskamp Institute, Neurodegenerative Disease and Proteomics Lab, Sarasota, FL (1)
Center for Diagbostik, Institute of Neuropathology, University Medical Center Hamburg Eppendorf, Germany (1)
State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau (1)
Fondazione Pisana per la Scienza ONLUS, 56107 San Giuliano Terme, Pisa, Italy Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands (1)
School of Life Science & Research Center for Natural Peptide Drugs, Shaanxi Engineering & Technological Research Centre for Conservation & Utilization of Regional Biological Resources, Yanan University (1)

IsPrivate

False (1)

Model Flag

Non Kinetic (1)

Classification

viruses (1)

Modification

4-tetrahydrothiazine-3-carboxylic acid (2)
79.966331 (1)
-17.026549 (1)
15.994915 (1)
57.021464 (1)
Not available (1)

Study type

Transcription profiling by array (503)
RNA-seq of coding RNA (136)
ChIP-seq (27)
RNA-seq of coding RNA from single cells (15)
RNA-seq of non coding RNA (14)
Methylation profiling by high throughput sequencing (12)
Methylation profiling by array (10)
Transcription profiling by SAGE (8)
Transcription profiling by RT-PCR (7)
Other (7)
Unknown experiment type (5)
ChIP-chip by tiling array (4)
Animal - High-throughput sequencing (4)
ChIP-chip by array (4)
Animal - One-color microarray (3)
RNA-seq of total RNA (3)
Cell line - Single-cell sequencing (1)
Cell line - High-throughput sequencing (1)
CLIP-seq (1)
MicroRNA profiling by high throughput sequencing (1)
Spatial transcriptomics by high-throughput sequencing (1)
Comparative genomic hybridization by array (1)
RIP-seq (1)
ScATAC-seq (1)
Single nucleus RNA sequencing (1)

Release Date

2021 (428)
2023 (408)
2024 (401)
2022 (385)
2025 (384)
2020 (352)
2018 (268)
2019 (256)
2017 (252)
2015 (248)
2016 (229)
2014 (213)
2013 (170)
2012 (126)
2011 (124)
2010 (92)
2008 (76)
2009 (60)
2026 (58)
2007 (43)
2005 (18)
2006 (12)
2003 (12)
2001 (8)
2000 (4)
2004 (2)
1999 (2)
1998 (2)
2002 (1)
1997 (1)

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Metabolomic signature of mouse cerebral cortex following Toxoplasma gondii infection

BACKGROUND: The protozoan parasite Toxoplasma gondii infects and alters the neurotransmission in cerebral cortex and other brain regions, leading to neurobehavioral and neuropathologic changes in humans and animals. However, the molecules that contribute to these changes remain l...

2020-04-23 | MTBLS770 | MetaboLights

A metabolome atlas of mouse brain on the global metabolic signature dynamics following short-term fasting

Calorie restriction (CR) or a fasting regimen is considered one of the most potent non-pharmacological interventions to prevent chronic metabolic disorders, ameliorate autoimmune diseases, and attenuate aging. Despite efforts, the mechanisms by which CR improves health, particularly brain health, ar...

2025-07-31 | MTBLS8006 | MetaboLights

High resolution analysis of genomic imprinting in the embryonic and adult mouse brain AND Sex-specific imprinting in the mouse brain

Genomic imprinting results in the preferential expression of the paternal, or maternal allele of certain genes. We have performed a genome-wide characterization of imprinting in the mouse embryonic and adult brain using F1 hybrid mice generated from reciprocal crosses of CASTEiJ and C57BL/6J mice. ...

ORGANISM(S): Mus musculus

2010-07-08 | E-GEOD-22131 | biostudies-arrayexpress

Changes in lipid profiles of epileptic mouse model

INTRODUCTION: Approximately 1% of the world's population is impacted by epilepsy, a chronic neurological disorder characterized by seizures. One-third of epileptic patients are resistant to AEDs, or have medically refractory epilepsy (MRE). One non-invasive treatment that exists...

2022-01-06 | MTBLS1432 | MetaboLights

Multi-Omics Analysis Reveals Alcohol exposure affects Ferroptosis pathway in Brain

Alcohol-related brain damage (ARBD) constitutes a major global public health issue and is often comorbid with neuropsychiatric disorders such as Alzheimer's and Parkinson's diseases. Ferroptosis, a form of regulated cell death characterized by iron dependency and lipid peroxidation, has been impl...

2026-03-11 | MTBLS14025 | MetaboLights

A Metabolome Atlas of the Aging Mouse Brain

Not available

ORGANISM(S): Mus musculus

ST001637 | MetabolomicsWorkbench

Targeted polyamine metabolomics of ATP13A4-deficient cellular and mouse models

ATP13A4 is a polyamine transporter enriched in astrocytes that regulates extracellular polyamine homeostasis. This study contains targeted LC-MS/MS metabolomics data from ATP13A4-deficient cellular and mouse models, including C8-D1A astrocytic cells, astrocyte-conditioned medium, mouse cortex, pl...

2026-06-10 | MTBLS14724 | MetaboLights

Monocolonization with Bacteroides thetaiotaomicron exerts region-specific effects on Alzheimer’s disease-related traits in the murine brain

Bacteroides thetaiotaomicron (B. theta) dominates the gut microbiome of most mammals. This strictly anaerobic gut symbiont colonizes the mucus layer of host intestinal epithelial cells in both healthy and diseased conditions. Reduced neuronal and vagal afferent innervation observed in ge...

2025-12-15 | MTBLS12896 | MetaboLights

Tryptophan metabolic disorder in gut-brain axis induces anxiety-like behavior via neuronal pyroptosis in mice exposed to radiofrequency radiation

Radiofrequency radiation (RFR) with specific parameters could alter brain function, yet the underlying mechanisms remain unclear. The gut-brain axis is reported to be important in regulating brain function. Therefore, this study used gut microbiota intervention, regulation of tryptophan metabolit...

2025-09-12 | MTBLS12482 | MetaboLights

Tryptophan metabolic disorder in gut-brain axis induces anxiety-like behavior via neuronal pyroptosis in mice exposed to radiofrequency radiation

2025-09-12 | MTBLS12483 | MetaboLights

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INTRODUCTION: Approximately 1% of the world's population is impacted by epilepsy, a chronic neurological disorder characterized by seizures. One-third of epileptic patients are resistant to AEDs, or have medically refractory epilepsy (MRE). One non-invasive treatment that exists...

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