Mouse cerebral cortex

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Unknown (1319)
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Mus musculus (661)
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mixed sample (3)
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Mus spretus (1)
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Organisms

Mus musculus (325)
Homo sapiens (26)
Mustela putorius furo (2)
Mus musculus musculus (2)
Macaca mulatta (2)
Rattus norvegicus (2)
Tupaia belangeri chinensis (1)
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gut metagenome (1)

Repository

biostudies-arrayexpress (457)
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geo (282)
pride (100)
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ExpressionAtlas (3)
dbGaP (2)
EGA (2)
MetabolomicsWorkbench (2)
PanoramaPublic (2)
GNPS (1)
PAXDB (1)

Tissue

Brain (69)
Cerebral cortex (19)
Hippocampus (5)
Liver (4)
Cerebellum (2)
Brown adipose tissue (2)
Brain (2)
Diaphragm (1)
Saliva-secreting gland (1)
Eye (1)
Embryonic tissue (1)
Skeletal muscle (1)
Olfactory bulb (1)
White adipose tissue (1)
Thymus (1)
Duodenum (1)
Colon (1)
Medulla oblongata (1)
Midbrain (1)
Stomach (1)
Pancreas (1)
Cortex of kidney (1)
Ovary (1)
Uterus (1)
Adrenal gland (1)
Ileum (1)
Renal medulla (1)
Spleen (1)
Lung (1)
Heart (1)

Disease

Alzheimer's disease (8)
Huntington Disease (3)
Disease free (3)
Cerebral ischemia (2)
Amyotrophic lateral sclerosis (2)
HIV encephalitis (1)
Normal (1)
Neuroblastoma (1)
Amyotrophic lateral sclerosis type 6 (1)
Subcortical band heterotopia (1)
Periventricular nodular heterotopia (1)
Carotid artery occlusion (1)
Cognitive impairment (1)
Epilepsy with generalized tonic-clonic seizures (1)
Progressive myoclonus epilepsy (1)
Alzheimer's disease 1 (1)
Zellweger syndrome (1)
Cerebrovascular disease (1)
Succinic semialdehyde dehydrogenase deficiency (1)
Neurological dysfunction (1)
Frontotemporal dementia (1)
Brain ischemia (1)
Neurodegenerative disease (1)
Down syndrome (1)
Obesity (1)
Autism spectrum disorder (1)
Parkinson's disease (1)
Brain cancer (1)
Breast cancer (1)

Technology Type

Mass Spectrometry (102)
Shotgun proteomics (45)
Bottom-up proteomics (32)
Data-independent acquisition (16)
Data-dependent acquisition (13)
Affinity purification coupled with mass spectrometry proteomics (9)
Mass spectrometry (8)
Mass spectrometry assay (4)
SWATH MS (4)
Gel-based experiment (3)
Top-down proteomics (3)
EI (2)
ESI (2)
Mass spectrometry imaging (1)
SRM/MRM (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (19)
Illumina HiSeq 2500 (15)
Orbitrap Fusion Lumos (8)
Illumina HiSeq 4000 (6)
NextSeq 500 (6)
Q Exactive HF (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)
NextSeq 2000 (2)
6550 iFunnel Q-TOF LC/MS (2)
Agilent 6550 QTOF (2)
LTQ Orbitrap Velos (2)
Q Exactive HF-X (2)
Chromium Next GEM Chip G (1)
10X v3 (1)
Illumina® (NEB, USA) (1)
Microcentrifuge (1)
MouseWG-6_V2_0_R3_11278593_A (1)
Ion Chef™ System and Ion S5™ System or Ion GeneStudio™ S5 Systems. (1)
ScanArray scanning hardware (1)
Illumina Genome Analyzer IIx (1)
Scanning hardware (1)
Illumina NovaSeq X (1)
Illumina MiniSeq (1)
N/a (1)
Ion Torrent S5 XL (1)
NextSeq 550 (1)
Illumina HiSeq 2000 (1)
Agilent 6550 Q-TOF (1)
Agilent 6550 qtof (1)
LTQ Velos ETD (1)

Publication Date

2015 (79)
2013 (68)
2016 (61)
2025 (59)
2022 (59)
2026 (55)
2024 (52)
2014 (50)
2011 (47)
2021 (43)
2012 (40)
2020 (39)
2010 (39)
2019 (38)
2023 (38)
2008 (32)
2018 (30)
2009 (21)
2017 (16)
2007 (13)
2006 (6)
2005 (6)
2003 (2)
2004 (1)

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)

CHEBI ID

CHEBI:16196 (4)
CHEBI:17351 (4)
CHEBI:71731 (3)
CHEBI:64424 (3)
CHEBI:18183 (3)
CHEBI:36005 (3)
CHEBI:15843 (3)
CHEBI:15756 (3)
CHEBI:16704 (3)
CHEBI:165867 (2)
CHEBI:181895 (2)
CHEBI:60366 (2)
CHEBI:134487 (2)
CHEBI:134445 (2)
CHEBI:71732 (2)
CHEBI:71723 (2)
CHEBI:71750 (2)
CHEBI:132673 (2)
CHEBI:71712 (2)
CHEBI:66860 (2)
CHEBI:134241 (2)
CHEBI:134270 (2)
CHEBI:16874 (2)
CHEBI:17242 (2)
CHEBI:17626 (2)
CHEBI:68454 (2)
CHEBI:30813 (2)
CHEBI:18133 (2)
CHEBI:32425 (2)
CHEBI:141588 (2)

Metabolite Name

Uridine (4)
Oleic acid (3)
Linoleic acid (3)
Hypoxanthine (3)
Citrulline (3)
Phenol, 2-[4-[(3,5-dichlorophenyl)amino]-6-methyl-2-pyrimidinyl]- (2)
Arachidonic sulfonic acid (2)
4(5H)-Thiazolone, 5-(6-quinolinylmethylene)-2-[(2-thienylmethyl)amino]-, (5Z)- (2)
7-Hydroxy-6-methoxy-3-methyl-5-(propan-2-ylidene)furo[2,3,4-de]chromen-2(5H)-one (2)
4-Amino-2-oxo-1,2-dihydropyrimidine-5-carboxylic acid (2)
Lys-Asp (2)
GDP-mannose (2)
Gamma-Glutamylglutamine (2)
Adenylsuccinic acid (2)
3-Methyl-1H-pyrazole-4-carbaldehyde (2)
PC(40:7) (2)
PC(38:5) (2)
Glutamate (2)
PE(P-36:4) (2)
6-Benzyl-3-butan-2-yl-9-(7-hydroxy-6-oxooctyl)-1,4,7,10-tetrazabicyclo[10.4.0]hexadecane-2,5,8,11-tetrone (2)
MES (2)
LPG(18:1(9Z)) (2)
Heptadecanoic acid (2)
Valine (2)
Ile-Leu (2)
Ala-Glu (2)
Pelargonic acid (2)
2-Aminopurine (2)
Pantothenol (2)
Putrescine (2)

First Public Date

2024 (48)
2025 (46)
2023 (44)
2019 (42)
2026 (38)
2022 (36)
2021 (35)
2014 (35)
2020 (31)
2017 (20)
2018 (18)
2015 (18)
2013 (5)
2016 (4)

Modification

4-tetrahydrothiazine-3-carboxylic acid (2)
-18.010565 (1)
-17.026549 (1)
42.010565 (1)
57.021464 (1)
Not available (1)

Study type

Transcription profiling by array (289)
RNA-seq of coding RNA (79)
ChIP-seq (19)
RNA-seq of coding RNA from single cells (13)
RNA-seq of non coding RNA (8)
Transcription profiling by SAGE (6)
Transcription profiling by RT-PCR (6)
Other (5)
Methylation profiling by array (5)
Unknown experiment type (3)
ChIP-chip by tiling array (3)
Animal - High-throughput sequencing (3)
Methylation profiling by high throughput sequencing (3)
Animal - One-color microarray (2)
ChIP-chip by array (2)
MicroRNA profiling by high throughput sequencing (2)
DNA-seq (2)
Cell line - Single-cell sequencing (1)
Whole chromosome random sequencing (1)
CLIP-seq (1)
Comparative genomic hybridization by array (1)
RIP-seq (1)
ScATAC-seq (1)
Single nucleus RNA sequencing (1)

Release Date

2021 (151)
2022 (133)
2015 (132)
2020 (129)
2023 (109)
2019 (109)
2024 (104)
2025 (99)
2018 (99)
2014 (99)
2013 (94)
2016 (88)
2017 (85)
2011 (71)
2012 (64)
2010 (58)
2008 (44)
2009 (30)
2026 (18)
2007 (17)
2005 (12)
2006 (10)
2003 (8)
2000 (4)
2004 (2)
2001 (2)
1997 (2)
2002 (1)
1999 (1)
1996 (1)

Lab affiliation

ULB Neuroscience Institute (UNI) Université Libre de Bruxelles (ULB) B-6041 Gosselies, Belgium. (2)
Central South University (2)
Department of Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA (2)
Hubei University of Medicine, Taihe Hospital (2)
State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau 999078 (1)
Department of Neuroscience , Tufts University (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)
Washington University in St. Louis - School of Medicine Division of Endocrinology, Metabolism & Lipid Research (1)
Division of Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität, Planegg-Martinsried, Germany. Institute of Stem Cell Research, Helmholtz Center Munich, Planegg-Martinsried, Germany. (1)
Department of Quantitative Biomedicine, University of Zurich, Switzerland (1)
Institute of Bioorganic Chemistry Polish Academy of Sciences in Poznan (1)
Queensland Brain Institute, Univerisity of Queensland (1)
Group Leader Proteostasis Charité Universitätsmedizin Berlin, Germany (1)
Neuron Glia Biology in Health and Disease Group, iMed.Ulisboa, Faculty of pharmacy, University of Lisbon, Lisbon, Portugal (1)
Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Japan (1)
Department of Microbiology and Immunology, Department of Biochemistry and Biophysics, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill (1)
Paris-Saclay Institute of Neuroscience, and CEA, Institut François Jacob, Université Paris-Saclay, Team Melki, CNRS, Gif-sur-Yvette, France (1)
Center for Neuroscience Research Children's National Medical Center 111 Michigan Avenue N.W., M7631 Washington, DC 20010-2970 Phone: +1-202-476-4279 Fax: +1-202-476-4988 e-mail: MTorii@childrensnational.org (1)
Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia (1)
Shenzhen eye hospital (1)
IMBA - Institute of Molecular Biotechnology GmbH Dr. Bohr-Gasse 3 1030 Vienna Austria (1)
Circadian Clock Project, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa 2-1-6, Setagaya-ku, Tokyo, 156-8506, Japan. (1)
Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiangan South Road, Xiamen, Fujian, 361102 P. R. China (1)
Head of the Mass Spectrometry and Proteomics facility (LSMP) at Institut Curie, France (1)
Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience,School of Medicine, Xiamen University, Xiangan South Road, Xiamen, Fujian, 361102 P. R. China (1)
Neurodegenerative Diseases Research Group, Korea Brain Research Institute (1)
1Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, 13 Vienna, Austria (1)
School of Biological Sciences. Division of Chemical Biology and Biotechnology. Nanyang Technological University. 60 Nanyang Drive, Singapore 637551 (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

Transcription profiling of different regions of E16.5 mouse cerebral cortex to identify region- and layer-specific genes.

The mammalian neocortex develops layer organizations with regional differences represented by expression of multiple genes at embryonic stages. These genes could play important roles in the formation of areal cyto-architecture, yet, the number of genes identified so far is not sufficient to explain ...

ORGANISM(S): Mus musculus

2007-12-13 | E-GEOD-929 | biostudies-arrayexpress

A comprehensive view of the transcriptome during development of the mouse cerebral cortex

The complexity of the mature adult brain is a result of both developmental processes and experience-dependent circuit formation. One way to look at the process of brain development is to examine gene expression changes, and previous studies have used microarrays to address this in a global manner. H...

ORGANISM(S): Mus musculus

2013-02-10 | E-GEOD-39866 | biostudies-arrayexpress

Single-cell RNA-seq of mouse cerebral cortex

We have applied a recently developed, highly accurate and sensitive single-cell RNA-seq method (STRT/C1) to perform a molecular census of two regions of the mouse cerebral cortex: the somatosensory cortex and hippocampus CA1. We isolated cells fresh from somatosensory cortex (S1) and hippocampus CA1...

ORGANISM(S): Mus musculus

2015-02-20 | E-GEOD-60361 | 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

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

Expression data from mouse cerebral cortex

Differential gene expression of cerebral cortex might be responsible for distinct neurovascular developments between different mouse strains We used Affymetrix microarray to explore the global gene expression patterns of mouse cerebral cortex of different mouse strains at two developmental stages Ce...

ORGANISM(S): Mus musculus

2013-10-21 | E-GEOD-46443 | biostudies-arrayexpress

Profiling of spatio-temporally regulated transcripts during cerebral corticogenesis in the mouse

The cerebral cortex plays an important role in cognitive function and specialized perception in mammals and its development requires highly specific spatio-temporal control of gene expression. The study identified stage- and region-specific markers throughout cerebral corticogenesis at various impor...

ORGANISM(S): Mus musculus

2009-09-25 | E-GEOD-15031 | biostudies-arrayexpress

Toxoplasma gondii infection induces metabolic alterations in the mouse cerebellum

Toxoplasma gondii is a protozoan parasite with a remarkable neurotropic affinity. We recently showed that T. gondii infection can alter the global metabolism of the cerebral cortex of the mice. However, the impact of this infection on the metabolism of the cerebellum remained unclear. In this study,...

2020-04-27 | MTBLS1537 | MetaboLights

Exposure to Propylthiouracil in Pregnant Mice Potentiates the Transcriptional Response to Thyroid Hormone in the Fetal Cerebral Cortex

Although the effects of thyroid hormones (TH) on the brain development have been extensively studied perinatally, effects of TH of maternal origin on the fetal brain development have been largely unexplored. We applied a high throughput study on the mouse models with aberrant TH levels on gestation ...

ORGANISM(S): Mus musculus

2014-02-04 | E-GEOD-43927 | biostudies-arrayexpress

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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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