Synapse composition

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Unknown (180)
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Organisms

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Organisms

Mus musculus (8)
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Repository

biostudies-arrayexpress (102)
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pride (23)
geo (14)
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Tissue

Brain (15)
T cell (4)
Blood (2)
Cell culture (2)
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Brain (1)
Astrocyte of the cerebral cortex (1)
Blood plasma (1)
Cell suspension culture (1)
Cerebral cortex (1)
Cerebral cortex pyramidal neuron (1)
Cerebrospinal fluid (1)
Hippocampal neuron (1)
Hippocampus (1)
Natural killer cell (1)
Neuron (1)
Neuron of cerebral cortex (1)
Primary cell (1)
Spleen (1)
Sternocleidomastoid muscle (1)
Synapse (1)
Synaptic membrane (1)

Disease

Schizophrenia (1)
Glioblastoma (1)
Amyotrophic lateral sclerosis (1)
Amyotrophic lateral sclerosis type 6 (1)
Disease free (1)
Down syndrome (1)
Duchenne muscular dystrophy (1)
Parkinson's disease (1)
Synucleinopathy (1)

Technology Type

Mass Spectrometry (23)
Shotgun proteomics (9)
Bottom-up proteomics (7)
Mass spectrometry assay (4)
Affinity purification coupled with mass spectrometry proteomics (4)
Data-dependent acquisition (4)
Mass spectrometry (3)
Gel-based experiment (3)
SWATH MS (2)
NMR spectroscopy (1)

Instrument Platform

Liquid Chromatography MS - positive - reverse phase (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 6000 (2)
Illumina HiSeq 2000 (2)
Illumina HiSeq 4000 (2)
Q Exactive HF (2)
Liquid Chromatography MS - positive - reverse-phase (2)
Liquid Chromatography MS - negative - reverse-phase (2)
Liquid Chromatography MS - negative - reverse phase (2)
Liquid Chromatography MS - negative - hilic (2)
Chromium Next GEM Chip G (1)
10X v3 (1)
Maxwell 16 (1)
Illumina Genome Analyzer IIx (1)
Ion Torrent Proton (1)
Illumina HiSeq 2500 (1)
LTQ Orbitrap Elite (1)
LTQ Orbitrap Velos (1)
Orbitrap Eclipse (1)
Orbitrap Fusion (1)
Q Exactive Plus (1)
Flow injection analysis MS - positive (1)
Nuclear Magnetic Resonance (NMR) - (1)
Liquid Chromatography MS - positive (1)
Liquid Chromatography MS - positive - hilic (1)
QExactive (1)

Publication Date

2015 (23)
2016 (18)
2026 (15)
2014 (13)
2013 (10)
2012 (9)
2010 (9)
2024 (8)
2022 (8)
2025 (7)
2011 (6)
2008 (6)
2021 (5)
2009 (4)
2007 (4)
2017 (2)
2018 (2)
2023 (2)
2004 (1)
2020 (1)

UNIPROT ID/AC

A0A024RC46 (1)
A0A087WT59 (1)
A0A087WTX5 (1)
A0A087WVW2 (1)
A0A087WVZ5 (1)
A0A087WWA5 (1)
A0A087WWK8 (1)
A0A087WXI0 (1)
A0A087WYL9 (1)
A0A087X130 (1)
A0A087X1S3 (1)
A0A087X1V9 (1)
A0A0A0MS07 (1)
A0A0A0MS51 (1)
A0A0C4DG89 (1)
A0A0C4DGT3 (1)
A0AVT1 (1)
A0FGR8 (1)
A0FGR8-2 (1)
A0FGR8-6 (1)
A0M8Q6 (1)
A0MZ66 (1)
A0N5G5 (1)
A0PJW6 (1)
A1L0T0 (1)
A2BFH1 (1)
A2IPI2 (1)
A2IPI5 (1)
A2J422 (1)
A2J423 (1)

ENSEMBL ID

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

CHEBI ID

CHEBI:15887 (2)
CHEBI:17497 (2)
CHEBI:16704 (2)
CHEBI:15891 (2)
CHEBI:17568 (2)
CHEBI:30915 (2)
CHEBI:17368 (2)
CHEBI:191894 (1)
CHEBI:89416 (1)
CHEBI:89059 (1)
CHEBI:35021 (1)
CHEBI:169166 (1)
CHEBI:36492 (1)
CHEBI:34131 (1)
CHEBI:34128 (1)
CHEBI:52386 (1)
CHEBI:46958 (1)
CHEBI:33993 (1)
CHEBI:88917 (1)
CHEBI:177252 (1)
CHEBI:170583 (1)
CHEBI:77694 (1)
CHEBI:177283 (1)
CHEBI:89513 (1)
CHEBI:89512 (1)
CHEBI:88918 (1)
CHEBI:177261 (1)
CHEBI:171349 (1)
CHEBI:81469 (1)
CHEBI:88990 (1)

Metabolite Name

2-Maleylacetate (2)
8-Hydroxyguanosine (2)
Glutamyltyrosine (2)
Calcidiol (2)
L-Histidine (2)
Taurine (2)
Prostaglandin J2 (2)
Deoxyinosine (2)
Inosine (2)
()-Pelletierine (1)
S-(3-Oxo-3-Carboxy-N-Propyl)Cysteine (1)
Methyl 5-[(5-Phenylthieno[2,3-D]Pyrimidin-4-Yl)Oxy]-2-Furoate (1)
Delphinidin 3-Glucoside (1)
Dopamine 4-Sulfate (1)
5-S-Glutathionyl-Aminochrome Reduced (1)
Kaempferol 3-O-Caffeoyl-Sophoroside 7-O-Glucoside (1)
6''-O-Alpha-D-Galactopyranosylciceritol (1)
Diosmetin-7-O-Beta-D-Glucopyranoside (1)
5-(4-Chlorophenyl)Sulfonyl-2-Methylpyrimidin-4-Amine (1)
Core Oligosaccharide (1)
4-(4-Chlorophenyl)-1-Phenyl-1,3-Dihydro-2H-Imidazole-2-Thione (1)
Ribavirin Monophosphate (1)
Kaempferol 3-(2'''-(E)-Caffeylsophoroside)-7-Glucoside (1)
Methionine Sulfone (1)
Kaempferol 3-O-Beta-Robinoside 7-O-Alpha-L-Rhamnopyranoside (1)
2-Isopropyl Citrate (1)
Genistein 4'-O-Glucoside (1)
Cyclohexaamylose (1)
Gailiapenta (1)
Sodium Benzofuran Isophthalate (1)

First Public Date

2026 (7)
2025 (6)
2024 (2)
2022 (2)
2016 (2)
2014 (2)
2023 (1)
2021 (1)
2018 (1)

Modification

-17.026549 (1)
15.994915 (1)
57.021464 (1)
79.966331 (1)

Study type

Transcription profiling by array (40)
RNA-seq of coding RNA (36)
ChIP-seq (7)
RNA-seq of non coding RNA (5)
Unknown experiment type (3)
Other (3)
RNA-seq of coding RNA from single cells (3)
Animal - High-throughput sequencing (1)
Transcription profiling by tiling array (1)
Comparative genomic hybridization by array (1)
Methylation profiling by array (1)
Methylation profiling by high throughput sequencing (1)

Release Date

2015 (31)
2016 (22)
2025 (21)
2024 (18)
2014 (18)
2021 (15)
2023 (14)
2022 (14)
2018 (13)
2013 (12)
2012 (12)
2010 (12)
2019 (12)
2008 (11)
2020 (11)
2011 (9)
2009 (9)
2007 (8)
2017 (7)
2026 (4)
2006 (4)
2004 (3)
2005 (1)
2002 (1)

Lab affiliation

Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine (CIPMM), Saarland University, 66421 Homburg, Germany (2)
Bernstein Professor Emeritus in Adult Psychiatry Department of Psychiatry and Behavioral Sciences University of Minnesota Medical School (1)
Biomolecular characterization unit, Center for Sustainable Resource Science, RIKEN (1)
Centre for Clinical Brain Sciences, University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK (1)
Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy (1)
Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (1)
Department of Molecular and Cellular Neurobiology, Center of Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, The Netherlands (1)
Department of Neuroscience , Tufts University (1)
Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA (1)
Department of Quantitative Biomedicine, University of Zurich, Switzerland (1)
Division of Systems and Cellular Medicine School of Medicine University of Dundee (1)
Institute of Physiology II Universität Freiburg Germany (1)
Institute of Physiology II University of Freiburg, Germany (1)
MRC - London Institute of Medical Sciences (1)
Prof. Dr. Henning Urlaub Max-Planck-Institute for Biophysical Chemistry Bioanalytical Mass Spectrometry Group Am Fassberg 11 D-37077 Goettingen, Germany University Medical Center Goettingen Bioanalytics Institute for Clinical Chemistry Robert Koch Strasse 40 D-37075 Goettingen, Germany (1)
Professor and Vivian L. Smith Endowed Chair in Neuroscience Department of Neuroscience. Baylor College of Medicine Houston, Texas United States (1)
School of Biosciences University of Sheffield Sheffield, S10 2TN United Kingdom (1)
Solomon H. Snyder Department of Neuroscience, Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA (1)
Target Discovery Institute, Nuffield Department of Medicine, University of Oxford (1)
University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry (1)
Yale University, New Haven, CT 06511 (1)
Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, USA (1)

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Expression profiles of globular bushy cells (GBCs) during maturation

Calyx of Held giant presynaptic terminals in the medial nucleus of the trapezoid body of the auditory brainstem form axosomatic synapses that have advanced to one of the best-studied synaptic system of the mammalian brain. As the auditory system matures and adjusts to high fidelity synaptic transmis...

ORGANISM(S): Rattus norvegicus

2014-06-24 | E-GEOD-49599 | biostudies-arrayexpress

Top3M-NM-2 is an RNA topoisomerase that works with Fragile X syndrome protein to promote synapse formation

Topoisomerases are crucial to solve DNA topological problems, but they have not been linked to RNA metabolism. Here we show that human topoisomerase 3M-NM-2 (Top3M-NM-2) is an RNA topoisomerase that biochemically and genetically interacts with FMRP, a protein deficient in Fragile X syndrome and know...

ORGANISM(S): Homo sapiens

2013-08-04 | E-GEOD-47502 | biostudies-arrayexpress

Mapping the dynamic high-density lipoprotein synapse

Background and aims: Heterogeneous high-density lipoprotein (HDL) particles, which can contain hundreds of proteins, affect human health and disease through dynamic molecular interactions with cell surface proteins. How HDL mediates its long-range signaling functions and interactions with various ce...

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

2022-11-17 | MSV000090734 | MassIVE

Proteomic studies of a single CNS synapse type: the parallel fiber/purkinje cell synapse.

Not available

S-EPMC2672601 | biostudies-literature

Integrated Proteomic and Multi-Omic Characterizations of the Synapse Reveal RNA Processing Factors and Ubiquitin Ligases Associated with Neurodevelopmental Disorders

The molecular composition of the excitatory synapse is incompletely defined due to its dynamic nature across developmental stages and neuronal populations. To address this gap, we apply proteomic mass spectrometry to characterize the synapse in multiple biological models including the fetal human br...

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

2026-03-09 | PXD020933 | Pride

Automated analysis of a diverse synapse population.

Not available

S-EPMC3610606 | biostudies-literature

Molecular, Phenotypic, and Sample-associated Data to Describe Pluripotent Stem Cell Lines and Derivatives

The use of induced pluripotent stem cells (iPSC) derived from independent patients and sources holds considerable promise to improve the understanding of development and disease. However, optimized use of iPSC depends on our ability to develop methods to efficiently qualify cell lines and protocols,...

ORGANISM(S): Homo sapiens

2016-08-20 | E-GEOD-85828 | biostudies-arrayexpress

Sleep maintains excitatory synapse diversity in the cortex and hippocampus.

Not available

S-EPMC11359089 | biostudies-literature

Integrated proteomic and multi-mic characterizations of the synapse reveal RNA processing factor and ubiquitin ligases associated with neurodevelopment disorders

ORGANISM(S): Homo sapiens

2025-03-28 | GSE228444 | GEO

PLA2G4E Orchestrates optimal Synapse Development and Neuronal Maturation [KO_Pla2g4e]

PRJNA1081123 | ENA

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