Synapses - OmicsDI

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synthetic construct (1)
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Organisms

Mus musculus (243)
Homo sapiens (71)
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Caenorhabditis elegans (3)
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mouse gut metagenome (1)
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Technology Type

Mass Spectrometry (163)
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Illumina HiSeq 2000 (2)
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Chemical cross-linking coupled with mass spectrometry proteomics (2)
Illumina Genome Analyzer II, Illumina HiSeq 2000 (1)
Affinity proteomics (1)
DiaPASEF (1)

Instrument Platform

Orbitrap Fusion Lumos (10)
Illumina NovaSeq 6000 (7)
Orbitrap Eclipse (5)
Illumina HiSeq 2500 (4)
Q Exactive HF-X (3)
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 HiSeq 4000 (2)
NextSeq 500 (2)
Instrument (2)
TripleTOF 6600 (2)
Direct infusion MS - positive (2)
Liquid Chromatography MS - positive - reverse-phase (2)
Liquid Chromatography MS - negative - reverse-phase (2)
Liquid Chromatography MS - negative - hilic (2)
Liquid Chromatography MS - negative - reverse phase (2)
Chromium Next GEM Chip G (1)
10X v3 (1)
Illumina MiniSeq (1)
NextSeq 2000 (1)
Q Exactive HFX (Thermo Scientific Instrument Model) (1)
Orbitrap Ascend (1)
LTQ Orbitrap XL (1)
Q Exactive HF (1)
TimsTOF Pro (1)
Q Exactive (1)
Direct infusion MS - negative (1)
Liquid Chromatography MS - alternating (1)
Liquid Chromatography MS - (1)
Liquid Chromatography MS - negative (1)

Publication Date

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2020 (41)
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2016 (26)
2018 (26)
2008 (23)
2015 (22)
2014 (22)
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2017 (19)
2011 (18)
2013 (17)
2012 (16)
2010 (15)
2006 (7)
2005 (4)
2009 (4)
2007 (4)
2004 (1)

UNIPROT ID/AC

Q9Z1X2 (2)
Q9Z0V2 (2)
Q9WVQ1 (2)
Q9WV18 (2)
Q9WU22 (2)
Q9WTK7 (2)
Q9R1C6 (2)
Q9R0N9 (2)
Q9QYK7 (2)
Q9QY40 (2)
Q9QUP5 (2)
Q9JMF3 (2)
Q9JME9 (2)
Q9JKL4 (2)
Q9JKF6 (2)
Q9JJV5 (2)
Q9ESN4 (2)
Q9EQZ6-3 (2)
Q9EQT6 (2)
Q9EPL2-2 (2)
Q9DCV5 (2)
Q9DCU2 (2)
Q9DBS2 (2)
Q9DAI2 (2)
Q9D938 (2)
Q9D6D0 (2)
Q9D4C9 (2)
Q9D3D0 (2)
Q9D387 (2)
Q9D365 (2)

ENSEMBL ID

ENSMUSP00000141542 (2)
ENSMUSP00000141097 (2)
ENSMUSG00000098557 (2)

CHEBI ID

CHEBI:15553 (4)
CHEBI:16027 (4)
CHEBI:16761 (4)
CHEBI:30915 (4)
CHEBI:28931 (3)
CHEBI:64561 (3)
CHEBI:16040 (3)
CHEBI:48928 (3)
CHEBI:17562 (3)
CHEBI:16750 (3)
CHEBI:15741 (3)
CHEBI:35697 (3)
CHEBI:17012 (3)
CHEBI:15891 (3)
CHEBI:15843 (3)
CHEBI:16704 (3)
CHEBI:16015 (3)
CHEBI:16919 (3)
CHEBI:17596 (3)
CHEBI:17368 (3)
CHEBI:36203 (2)
CHEBI:72736 (2)
CHEBI:28315 (2)
CHEBI:18148 (2)
CHEBI:45979 (2)
CHEBI:9334 (2)
CHEBI:79317 (2)
CHEBI:17226 (2)
CHEBI:7823 (2)
CHEBI:50202 (2)

Metabolite Name

Cytosine (3)
11,12-EET (2)
S-Lactoylglutathione (2)
PGF2a (2)
Uracil (2)
Thiabendazole (2)
Niacinamide (2)
Gamma-Aminobutyric acid (2)
L-Proline (2)
Adenosine monophosphate (2)
Trans-Cinnamic acid (2)
Maleic acid (2)
L-Histidine (2)
L-Glutamic acid (2)
Taurine (2)
Oxypurinol (2)
Adenosine (2)
Oleic acid (2)
Cytidine (2)
Creatine (2)
L-Carnitine (2)
L-Leucine (2)
Inosine (2)
Hypoxanthine (2)
17R-Resolvin (1)
PD1 (1)
7(R)Marisin1 (1)
10(S),17(s)-DiHDoHE (1)
Resolvin-D2 (1)
Resolvin-D1 (1)

First Public Date

2025 (81)
2024 (53)
2026 (52)
2023 (47)
2021 (34)
2014 (34)
2020 (28)
2022 (23)
2019 (21)
2018 (18)
2017 (15)
2016 (9)
2015 (5)
2013 (3)

Modelling Approach

Ordinary differential equation model (5)

Lab affiliation

Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany (4)
Aarhus University Hospital, Denmark (3)
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)
Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, The Netherlands (3)
Laboratory of Molecular Basis of Synaptic Plasticity Centre of New Technologies, University of Warsaw (2)
Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany (2)
Molecular Physiology of the Synapse Laboratory Institut de Recerca Sant Pau (IR Sant Pau) C/Sant Quintí, 77-79 08041 Barcelona Spain (2)
Leibniz-Forschungsinstitut für Molekulare Pharmakologie (2)
Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China (2)
MPIs for Biophysics and Brain Research (2)
Lab of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil (2)
MPIs for Brain Research and Biophysics (2)
Institute of Physiology II, University of Freiburg, Germany (2)
Max Planck Institute for Brain Research Max Planck Institute of Biophysics (2)
Head of the Curie Institute Mass Spectrometry Platform (2)
Freie Universität Berlin (1)
Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences.Shenzhen 518055，China (1)
Department of Neuroscience , Tufts University (1)
Institut du Fer a Moulin, Inserm-Sorbonne Université UMR-S 1270, Paris, France (1)
Center for Diagbostik, Institute of Neuropathology, University Medical Center Hamburg Eppendorf, Germany (1)
95 Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, 31077, France (1)
The Solomon H. Snyder Department of Neuroscience Johns Hopkins University School of Medicine USA (1)
Neurology Department, Experimental Research in Stroke and Inflammation (ERSI) group, University Medical Center Hamburg-Eppendorf, Hamburg, Germany (1)
Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia (1)
Department of Quantitative Biomedicine, University of Zurich, Switzerland (1)
Ruhr-University Bochum, Zentrum für Proteindiagnostik (ProDi), Medizinisches Proteom-Center (MPC) (1)
University of Oslo, Oslo University Hospital, University of Lübeck, University of Latvia, Tel Aviv University www.pahnkelab.eu (1)
Synapse Development and Plasticity Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, Quebec, H2W 1R7, Canada Integrated Program in Neuroscience, McGill University, Montreal, Quebec, H3A 2B2, Canada Department of Medicine, Université de Montréal, Montreal, Quebec, H3T 1J4, Canada Division of Experimental Medicine, McGill University, Montreal, Quebec, H3A 0G4, Canada (1)
University of Vienna Department of Chemistry Institute of Analytical Chemistry (1)
Fondazione Pisana per la Scienza (1)

IsPrivate

False (5)

Modification

2x(15)N labeled L-lysine (1)
4x(15)N labeled L-arginine (1)
4-tetrahydrothiazine-3-carboxylic acid (1)

Study type

Transcription profiling by array (81)
RNA-seq of coding RNA (20)
ChIP-seq (6)
RNA-seq of coding RNA from single cells (4)
Unknown experiment type (3)
Methylation profiling by array (3)
Animal - High-throughput sequencing (2)
Other (2)
RNA-seq of non coding RNA (2)
ChIP-chip by tiling array (1)
CLIP-seq (1)
MicroRNA profiling by high throughput sequencing (1)
Spatial transcriptomics by high-throughput sequencing (1)
Comparative genomic hybridization by array (1)
Methylation profiling by high throughput sequencing (1)

Release Date

2021 (728)
2023 (711)
2022 (665)
2025 (656)
2024 (589)
2020 (521)
2019 (503)
2018 (503)
2017 (459)
2016 (423)
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2013 (220)
2012 (217)
2010 (212)
2011 (189)
2009 (162)
2008 (146)
2006 (84)
2026 (82)
2007 (79)
2004 (58)
2005 (41)
2003 (27)
2002 (21)
2000 (15)
1999 (12)
2001 (11)
1997 (7)
1998 (4)

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Transcription profiling of rat control subplate neurons with few synapses and cocultured subplate neurons with induced synaptogenesis

The transcriptional events accompanying synaptogenesis are largely unknown, or have been studied in systems in which synapse formation occurs gradually over time. With a system in which synaptogenesis is synchronized and controllable, molecular or biochemical techniques can be used to examine cellu...

ORGANISM(S): Rattus norvegicus

2008-11-29 | E-GEOD-8318 | biostudies-arrayexpress

Homer1a drives Homeostatic Scaling-down of Excitatory Synapses During Sleep

Homeostatic scaling is a global form of synaptic plasticity used by neurons to adjust overall synaptic weight and maintain neuronal firing rates while protecting information coding. While homeostatic scaling has been demonstrated in vitro, a clear physiological function of this plasticity type has n...

ORGANISM(S): Mus musculus (Mouse)

2017-02-13 | PXD004537 | Pride

Synaptopodin regulates denervation-induced plasticity at hippocampal mossy fiber synapses

PRJNA894142 | ENA

ADGRB1 contributes to astrocyte-mediated phagocytosis of excitatory synapses

PRJNA1073438 | ENA

The amyloid precursor protein regulates synaptic transmission at medial perforant path synapses

PRJNA880333 | ENA

Spectrin-beta 2 facilitates the selective accumulation of GABAA receptors at somatodendritic synapses

Fast synaptic inhibition is dependent on targeting specific GABAAR subtypes to dendritic and axon initial segment (AIS) synapses. Synaptic GABAARs are typically assembled from 1-3, and subunits. Here, we isolate distinct GABAARs from the brain and interrogate their composition using quantitative pr...

ORGANISM(S): Mus musculus (Mouse)

2023-03-10 | PXD038703 | Pride

Ais Gaba a receptors Spectrins

Optogenetics and electron tomography for structure-function analysis of cochlear ribbon synapses.

Not available

S-EPMC9908081 | biostudies-literature

High-Throughput Transcriptome Profiling of Single Nuclei and Single Synapses Using Single-Cell Total-RNA-Seq [Hs]

PRJNA729162 | ENA

High-Throughput Transcriptome Profiling of Single Nuclei and Single Synapses Using Single-Cell Total-RNA-Seq [Mm]

PRJNA819431 | ENA

A Dach2-Hdac9-Myog-Gdf5 signaling system regulates regeneration of neuromuscular synapses

Muscle denervation due to injury, disease or aging results in impaired motor function. Restoring neuromuscular communication requires axonal regrowth and regeneration of neuromuscular synapses. Muscle activity inhibits neuromuscular synapse regeneration. The mechanism by which muscle activity regu...

ORGANISM(S): Mus musculus

2015-10-29 | E-GEOD-58669 | biostudies-arrayexpress

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