Cerebral cortex

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Unknown (7553)
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Organisms

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mixed sample (4)
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Mus musculus domesticus (1)
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Organisms

Mus musculus (521)
Homo sapiens (149)
Rattus norvegicus (48)
Macaca mulatta (15)
Mustela putorius furo (7)
Sus scrofa (5)
Gallus gallus (5)
Macaca fascicularis (4)
Ovis aries (3)
Pleurodeles waltl (2)
Tupaia belangeri chinensis (2)
Callithrix jacchus (2)
Papio anubis (2)
Mus musculus musculus (2)
Papio hamadryas (1)
Synthetic plasmid (1)
Pan troglodytes (1)
Heterocephalus glaber (1)
Chlorocebus sabaeus (1)
unidentified (1)
Drosophila melanogaster (1)
Canis lupus familiaris (1)
Felis catus (1)
gut metagenome (1)

Repository

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dbGaP (11)
PAXDB (8)
MetabolomicsWorkbench (7)
PanoramaPublic (3)
BioModels (2)
GNPS (2)
Cell Collective (1)

Tissue

Cerebral cortex (37)
Liver (12)
Stomach (10)
Pancreas (10)
Hippocampus (10)
Lung (9)
Cerebellum (9)
Kidney (9)
Ovary (8)
Spleen (8)
Testis (8)
Colon (7)
Prostate gland (7)
Adrenal gland (7)
Heart (7)
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Esophagus (6)
Uterus (6)
Thyroid gland (6)
Lymph node (6)
Spinal cord (6)
Small intestine (5)
Duodenum (5)
Skeletal muscle tissue (5)
Urinary bladder (5)
Skin (5)
Bone marrow (4)
Endometrium (4)
Fallopian tube (4)
Vagina (4)

Disease

Normal (9)
Rheumatoid arthritis (2)
Hepatocellular carcinoma (2)
Melanoma (2)
Secondary progressive multiple sclerosis (1)
Cortical ischemic stroke (1)
Transient gestational hypothyroxinemia and recovery of physiological levels of thyroid homone (1)
Transient gestational hyperthyroxinemia (1)
Transient gestational hypothyroxinemia (1)
Meningeal tuberculosis (1)
Alzheimers disease (1)
Adenocarcinoma (1)
Adenomyosis (1)
Uterine fibroid (1)
Neuromuscular pain (1)
Endometriosis (1)
Normal - esophagus muscularis mucosa (GTEx) (1)
Normal - uterus (GTEx) (1)
Normal - adjacent to lung adenocarcinoma (1)
Normal - suprapubic skin (GTEx) (1)
Normal - adjacent to prostate adenocarcinoma (1)
Normal - adjacent to head and neck squamous cell carcinoma (1)
Normal - urinary bladder (GTEx) (1)
Normal - C1 segment of cervical spinal cord (GTEx) (1)
Normal - adjacent to squamous cell lung carcinoma (1)
Normal - prostate gland (GTEx) (1)
Normal - breast (GTEx) (1)
Normal - nucleus accumbens (GTEx) (1)
Normal - adjacent to breast adenocarcinoma (1)
Normal - cerebral cortex (GTEx) (1)

Technology Type

Mass Spectrometry (161)
Shotgun proteomics (75)
Bottom-up proteomics (44)
Data-dependent acquisition (20)
Data-independent acquisition (19)
Affinity purification coupled with mass spectrometry proteomics (15)
Mass spectrometry (13)
Mass spectrometry assay (6)
ESI (6)
SWATH MS (6)
Gel-based experiment (5)
Top-down proteomics (5)
NMR spectroscopy (3)
EI (2)
SRM/MRM (2)
Illumina HiSeq 2500, ILLUMINA (1)
Illumina HiSeq 2500, ILLUMINA, Illumina HiSeq 2000 (1)
MALDI (1)
Metaproteomics (1)
Proteogenomics (1)
Mass spectrometry imaging (1)
Immunopeptidomics (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (28)
Illumina HiSeq 2500 (21)
Illumina HiSeq 4000 (12)
NextSeq 500 (7)
NextSeq 2000 (3)
Illumina HiSeq 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)
Chemostat (2)
Affymetrix (2)
Illumina NovaSeq X (2)
NextSeq 550 (2)
Chromium Next GEM Chip G (1)
10X v3 (1)
Nanopore sequencing (1)
BD Rhapsody (1)
Illumina® (NEB, USA) (1)
Microcentrifuge (1)
454 GS FLX (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)
G2565AA DNA microarray scanner [Agilent] (1)
Illumina Genome Analyzer IIx (1)
Illumina Genome Analyzer II (1)
Scanning hardware (1)
Illumina MiniSeq (1)
N/a (1)
Nanodrop spectrophotometer (1)
No (1)
MinION (1)

Publication Date

2022 (153)
2026 (141)
2015 (122)
2025 (119)
2024 (101)
2013 (100)
2023 (98)
2021 (93)
2016 (93)
2012 (92)
2011 (77)
2019 (75)
2014 (75)
2020 (72)
2010 (66)
2008 (57)
2018 (53)
2009 (44)
2017 (38)
2007 (25)
2006 (11)
2005 (10)
2004 (3)
2003 (3)

UNIPROT ID/AC

Q9BQG2 (2)
B3KXN9 (2)
Q53HM1 (2)
Q9HBF5 (2)
Q86SK9 (2)
E9KL42 (2)
Q3I5F7 (2)
P33897 (2)
Q99884 (2)
A8MU28 (2)
P35219 (2)
Q5FC00 (2)
B2RBR4 (2)
Q8WUM9 (2)
Q15274 (2)
Q8WWX8 (2)
Q9NX14 (2)
Q9Y345 (2)
Q86YT5 (2)
Q53H96 (2)
E9PHN8 (2)
Q9NWU1 (2)
Q96C36 (2)
Q9NP59 (2)
Q9NRX3 (2)
Q9UBF8 (2)
B4DYG5 (2)
P38571 (2)
O75610 (2)
Q6UWQ5 (2)

CHEBI ID

CHEBI:3338 (2)
CHEBI:3966 (2)
CHEBI:3312 (2)
CHEBI:3313 (2)
CHEBI:3628 (2)
CHEBI:3454 (2)
CHEBI:3544 (2)
CHEBI:4541 (2)
CHEBI:3322 (2)
CHEBI:3729 (2)
CHEBI:3420 (2)
CHEBI:3303 (2)
CHEBI:3513 (2)
CHEBI:3339 (2)
CHEBI:58235 (2)
CHEBI:3793 (2)
CHEBI:36986 (2)
CHEBI:58052 (2)
CHEBI:18402 (2)
CHEBI:57880 (2)
CHEBI:57367 (2)
CHEBI:30913 (2)
CHEBI:57363 (2)
CHEBI:58454 (2)
CHEBI:57373 (2)
CHEBI:28508 (2)
CHEBI:28095 (2)
CHEBI:57795 (2)
CHEBI:58480 (2)
CHEBI:11892 (2)

Metabolite Name

Uridine (6)
L-alanine (4)
Hypoxanthine (4)
Citrulline (4)
Glycine (4)
Inosine (4)
3-hydroxybutyric acid (3)
L-isoleucine (3)
Ethanolamine (3)
L-tyrosine (3)
L-glutamine (3)
L-threonine (3)
L-phenylalanine (3)
L-valine (3)
Putrescine (3)
Capric acid (3)
Allantoin (3)
Pantothenic acid (3)
Catechin (3)
Deoxycholic acid (3)
Citric acid (3)
Stearic acid (3)
Isocitric acid (3)
Glyceric acid (3)
Malic acid (3)
Homoserine (3)
Oleamide (3)
Pipecolic acid (3)
Serine (3)
Palmitic acid (3)

First Public Date

2024 (118)
2025 (111)
2014 (97)
2026 (87)
2023 (86)
2022 (76)
2020 (71)
2019 (68)
2021 (62)
2017 (46)
2018 (35)
2015 (33)
2016 (19)
2013 (12)

Lab affiliation

Paris-Saclay Institute of Neuroscience, Team Melki, CNRS, Gif-sur-Yvette, France (4)
DZNE Munich, Neuroproteomics, Feodor-Lynen-Str. 17, 81377 München, Germany (3)
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)
Bernstein Professor Emeritus in Adult Psychiatry Department of Psychiatry and Behavioral Sciences University of Minnesota Medical School (2)
Developmental Neurobiology, Max Planck Institute of Psychiatry, Munich, Germany (1)
Department of Pediatrics University of Maryland, School of Medicine (1)
State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau 999078 (1)
Cambridge Centre for Proteomics University of Cambridge (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)
Department of Rehabilitation Medicine, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China (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)
Dept Clinical and Experimental Medicine, University of Catanzaro, Viale Europa, 88100 Catanzaro (Italy) (1)
Research and Development, NHS Blood and Transplant Nuffield Department of Surgical Sciences, and Oxford Biomedical Research Centre, University of Oxford (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)
Mount Sinai Hospital (Lab Head) (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)

IsPrivate

False (2)

Model Flag

Non Kinetic (2)

Modification

4-tetrahydrothiazine-3-carboxylic acid (3)
Not available (2)
-18.010565 (1)
-17.026549 (1)
42.010565 (1)
N6 (1)
N6-dimethyl-L-lysine (1)
57.021464 (1)

Study type

Transcription profiling by array (444)
RNA-seq of coding RNA (113)
RNA-seq of coding RNA from single cells (25)
ChIP-seq (22)
RNA-seq of non coding RNA (20)
Methylation profiling by array (17)
Transcription profiling by SAGE (7)
Unknown experiment type (7)
Other (7)
Transcription profiling by RT-PCR (6)
Methylation profiling by high throughput sequencing (5)
Animal - High-throughput sequencing (4)
DNA-seq (4)
Animal - One-color microarray (3)
ChIP-chip by tiling array (3)
Human - One-color microarray (2)
ChIP-chip by array (2)
MicroRNA profiling by high throughput sequencing (2)
ScATAC-seq (2)
RNA-seq of total RNA (2)
Cell line - Single-cell sequencing (1)
Human - High-throughput sequencing (1)
Whole chromosome random sequencing (1)
Genotyping by array (1)
CLIP-seq (1)
Comparative genomic hybridization by array (1)
RIP-seq (1)
Single nucleus RNA sequencing (1)
MicroRNA profiling by array (1)

Release Date

2022 (807)
2021 (799)
2023 (784)
2020 (744)
2024 (588)
2025 (568)
2018 (508)
2019 (504)
2017 (454)
2015 (440)
2016 (394)
2014 (317)
2013 (230)
2012 (207)
2011 (187)
2010 (181)
2008 (144)
2009 (136)
2026 (66)
2007 (54)
2006 (39)
2005 (35)
2003 (21)
2000 (11)
2004 (10)
2001 (9)
2002 (7)
1999 (6)
1998 (5)
1997 (3)

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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

Transcriptomics Responses to Hypoxia and Ketamine in Ovine Fetal Cerebral Cortex

Transient hypoxia in pregnancy stimulates a physiological reflex response that redistributes blood flow and defends oxygen delivery to the fetal brain. The chemoreceptor reflex that is responsible for this physiological response is dependent on glutamatergic neurotransmission which, in times of vig...

ORGANISM(S): Ovis aries

2016-04-06 | E-GEOD-76110 | 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

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

Human and Rhesus macaque cerebral cortex DNA methylation by MeDIP-Chip

This SuperSeries is composed of the following subset Series: GSE27459: Human cerebral cortex DNA methylation by MeDIP-Chip GSE27460: Rhesus macaque cerebral cortex DNA methylation profiling by MeDIP-Chip Refer to individual Series

ORGANISM(S): Macaca mulatta

2012-03-01 | E-GEOD-27461 | biostudies-arrayexpress

Lipidomics analysis for aged mice brain cortex (part-II)

Not available

ORGANISM(S): Mus musculus

ST001065 | MetabolomicsWorkbench

Patterns of gene expression and evolution in the human developing cerebral cortex

The cerebral cortex underwent a rapid expansion and complexification during recent primate evolution, but the underlying developmental mechanisms remain essentially unknown. In order to uncover genetic networks underlying the development of the human cerebral cortex, we profiled the transcriptome o...

ORGANISM(S): Homo sapiens

2011-06-01 | E-GEOD-21858 | 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

Effects of diet and age on canine cerebral cortex gene expression

Mechanisms contributing to age-related cognitive decline are poorly defined. Thus, we used canine microarrays to compare gene expression profiles of brain tissue from geriatric and young adult dogs. Cerebral cortex samples were collected from 6 geriatric (12 yr-old) and 6 young adult (1 yr-old) fe...

ORGANISM(S): Canis lupus familiaris

2008-08-05 | E-GEOD-12328 | biostudies-arrayexpress

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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