Primary cortical neurons

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Unknown (1974)
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Organisms

Mus musculus (353)
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Tissue

Brain (32)
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Primary cerebral cortical neuronï¿½ (4)
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Cerebral cortex (2)
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Hypothalamic nucleus (1)
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Neural tissue (1)

Disease

Parkinson's disease (4)
Alzheimer's disease (2)
Amyotrophic lateral sclerosis (2)
Normal (1)
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Charcot-Marie-Tooth disease (1)
Disease free (1)
FTDALS1 (1)
Fragile X syndrome (1)
Frontotemporal dementia (1)
Huntington Disease (1)
Leukoencephalopathy with vanishing white matter (1)
Neurodegenerative disease (1)

Technology Type

Mass Spectrometry (67)
Shotgun proteomics (41)
Affinity purification coupled with mass spectrometry proteomics (16)
Bottom-up proteomics (12)
Data-dependent acquisition (4)
Top-down proteomics (4)
Mass spectrometry (3)
Data-independent acquisition (3)
Gel-based experiment (2)
Mass spectrometry assay (1)
HDMSE (1)
SWATH MS (1)

Instrument Platform

Illumina NovaSeq 6000 (23)
Illumina HiSeq 2500 (12)
NextSeq 500 (12)
Illumina HiSeq 4000 (5)
NextSeq 550 (4)
Orbitrap Fusion Lumos (4)
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)
-- (1)
Chromium Next GEM Chip G (1)
10X v3 (1)
Nanopore sequencing (1)
Qubit 4.0 and TapeStation (1)
Element AVITI (1)
MA900, Sony (1)
Cutadapt, STAR (1)
TruSeq Stranded mRNA Sample Prep Kit (Illumina) (1)
BD InFlux Cytometer (Becton-Dickinson) (1)
10x Chromium Controller (1)
Not applicable (1)
Illumina NovaSeq X (1)
Illumina MiniSeq (1)
NextSeq 2000 (1)
MinION (1)
6560 Q-TOF LC/MS (1)
Exactive (1)
Orbitrap Astral (1)
Orbitrap Eclipse (1)
Orbitrap Fusion Tribrid (Thermo Scientific instrument model) (1)
Q Exactive (1)
Q Exactive HF (1)

Publication Date

2020 (114)
2023 (99)
2024 (58)
2026 (38)
2025 (37)
2013 (36)
2015 (34)
2021 (32)
2022 (26)
2016 (26)
2012 (19)
2018 (18)
2014 (16)
2019 (14)
2008 (13)
2011 (12)
2009 (11)
2007 (10)
2006 (6)
2017 (5)
2010 (5)
2005 (1)

UNIPROT ID/AC

Q08999 (2)
P11802 (2)
Q01094 (2)
P24941 (2)
P24864 (2)
P24385 (2)
10116.ENSRNOP00000000015 (1)
10116.ENSRNOP00000003558 (1)
10116.ENSRNOP00000004657 (1)
10116.ENSRNOP00000012904 (1)
10116.ENSRNOP00000013100 (1)
10116.ENSRNOP00000018309 (1)
10116.ENSRNOP00000022328 (1)
10116.ENSRNOP00000023502 (1)
10116.ENSRNOP00000038798 (1)
10116.ENSRNOP00000041168 (1)
10116.ENSRNOP00000050143 (1)
10116.ENSRNOP00000050794 (1)
10116.ENSRNOP00000057948 (1)
10116.ENSRNOP00000059474 (1)
10116.ENSRNOP00000061523 (1)
10116.ENSRNOP00000062001 (1)
10116.ENSRNOP00000065069 (1)
10116.ENSRNOP00000066087 (1)
10116.ENSRNOP00000066126 (1)
10116.ENSRNOP00000067294 (1)
10116.ENSRNOP00000067711 (1)
1433B_RAT (1)
1433E_RAT (1)
1433F_RAT (1)

CHEBI ID

CHEBI:15422 (5)
CHEBI:15996 (3)
CHEBI:17552 (3)
CHEBI:16761 (3)
CHEBI:16908 (3)
CHEBI:47867 (2)
CHEBI:16595 (2)
CHEBI:16541 (2)
CHEBI:29108 (2)
CHEBI:38262 (2)
CHEBI:30860 (2)
CHEBI:18321 (2)
CHEBI:70959 (2)
CHEBI:18075 (2)
CHEBI:24266 (2)
CHEBI:17626 (2)
CHEBI:29042 (2)
CHEBI:16974 (2)
CHEBI:40410 (2)
CHEBI:17992 (2)
CHEBI:73061 (2)
CHEBI:32365 (2)
CHEBI:18066 (2)
CHEBI:17172 (2)
CHEBI:17200 (2)
CHEBI:25722 (2)
CHEBI:17553 (2)
CHEBI:44215 (2)
CHEBI:29019 (2)
CHEBI:50129 (2)

Metabolite Name

Acetoacetic acid (2)
GTP (2)
Acetyl-CoA (2)
ATP (2)
AMP (2)
Uracil (2)
ADP (2)
NADP (2)
NADPH (2)
NAD (2)
Phosphoenolpyruvate (2)
Taurine (2)
GDP (2)
DTMP (2)
3-Hydroxybutyric acid (2)
Succinate (2)
Sarcosine (2)
NADH (2)
Adenine (2)
Pyruvate (2)
Cytidine (2)
Guanosine (2)
Uridine (2)
Inosine (2)
Glutathione oxidized (GSSG) (1)
UDP-N-Acetylgalactosamine (1)
UDP-Glucuronic acid (1)
1,2-Dipalmitin (1)
DTDP-Glucose (1)
Taurolithocholic Acid (1)

First Public Date

2020 (115)
2023 (90)
2024 (52)
2026 (40)
2025 (40)
2014 (34)
2022 (28)
2021 (22)
2018 (17)
2019 (12)
2015 (11)
2017 (9)
2016 (7)
2013 (2)

Modelling Approach

Ordinary differential equation model (2)

Lab affiliation

Cell Biology and Physiology, University of North Carolina at Chapel Hill, North Carolina, USA (2)
Department of Chemistry and Biotechnology Tallinn University of Technology Estonia (2)
MPIs for Biophysics and Brain Research (2)
Biogen (1)
Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark (1)
Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK (1)
Cellzome (1)
Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Québec, QC, Canada Centre de recherche sur le cancer de l’Université Laval, Québec, QC, Canada PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada (1)
Chiara Guerrera, IRHC, HDR Head of the Necker Proteomics Faculty of Medecine, University Paris Cité SFR Necker INSERM US24 160 rue de Vaugirard | 75015 Paris Tél. 01 40 61 54 6 (1)
Core Unit Proteomics, BIH at Charite and MDC, Robert Roessle Strasse 10, 13125 Berlin (1)
DZNE Munich, Neuroproteomics, Feodor-Lynen-Str. 17, 81377 München, Germany (1)
DZNE: German center for Neurodegenerative Diseases, Munich, https://www.dzne.de/index.php?id=105&L=1 (1)
Dana Farber Cancer Institute, Boston, MA Harvard Medical School, Boston, MA (1)
Department of Biochemistry and Molecular Biology Bio21 Molecular Science and Biotechnology Institute Cell Signalling Research Laboratories The University of Melbourne Parkville, Victoria 3010, Australia (1)
Department of Biochemistry and Molecular Biology The University of Melbourne Australia (lab head) (1)
Department of Health Sciences and Technology (D-HEST) Institute of Molecular Systems Biology (IMSB) ETH Zürich (1)
Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel (1)
Department of Life Sciences, University of Bath, UK (1)
Department of Neurological Surgery, Washington University in St. Louis School of Medicine (1)
Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA (1)
Department of Pathology, Amsterdam University Medical Centres, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Amsterdam, The Netherlands (1)
Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai (1)
Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany. NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark. (1)
Dept. Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Munich, Germany (1)
Director of Research Head, Signalling and Transcription Group The Francis Crick Institute 1 Midland Road, London NW11AT, UK (1)
German Center for Neurodegenerative Diseases (DZNE) Munich (1)
Group Leader Proteostasis Charité Universitätsmedizin Berlin, Germany (1)
Group leader, Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands (1)
Hannover Medical School (1)
IRCCS Istituto G Gaslini (1)

IsPrivate

False (2)

Modification

2x(15)N labeled L-lysine (1)
4x(15)N labeled L-arginine (1)

Study type

Transcription profiling by array (96)
RNA-seq of coding RNA (67)
ChIP-seq (11)
RNA-seq of coding RNA from single cells (11)
Ribo-seq (3)
Other (3)
Methylation profiling by high throughput sequencing (3)
RNA-seq of total RNA (3)
ChIP-chip by tiling array (2)
Cell line - Single-cell sequencing (1)
Animal - High-throughput sequencing (1)
Cell line - High-throughput sequencing (1)
Genotyping by array (1)
Capture-C (1)
MicroRNA profiling by high throughput sequencing (1)
Spatial transcriptomics by high-throughput sequencing (1)
ATAC-seq (1)
Single nucleus RNA sequencing (1)
Methylation profiling by array (1)
RNA-seq of non coding RNA (1)

Release Date

2023 (209)
2025 (201)
2021 (197)
2022 (173)
2024 (166)
2019 (151)
2020 (144)
2016 (124)
2018 (114)
2015 (108)
2017 (100)
2013 (76)
2014 (75)
2012 (63)
2011 (61)
2010 (44)
2009 (42)
2026 (37)
2008 (35)
2007 (22)
2006 (11)
2003 (6)
2005 (5)
2004 (5)
2002 (4)
2000 (3)
1999 (3)
2001 (2)
1998 (1)
1997 (1)

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Single cell transcriptomics analysis of induced pluripotent stem cell-derived cortical neurons reveals frequent dual layer identity

Induced pluripotent stem cell (iPSC)-derived cortical neurons present a powerful new model of neurological disease. Previous work has established that differentiation protocols produce cortical neurons but little has been done to characterise these at cellular resolution. In particular, it is unclea...

ORGANISM(S): Homo sapiens

2016-01-08 | E-GEOD-69790 | biostudies-arrayexpress

Expression profiles of primary cortical neurons after knocking down Fus

To clarify the functional properties of FUS, we established the differentially expressed alternative exons in FUS-silenced primary cortical neurons by using exon-sensitive microarray technology. We analyzed total RNA of primary cortical neuron infected with lentivirus expressing shRNA against mouse ...

ORGANISM(S): Mus musculus

2012-07-23 | E-GEOD-36153 | biostudies-arrayexpress

RNA-seq of human and mouse stem-cell derived neurons and mouse primary cortical neurons after KCl-induced membrane depolarization against controls.

This experiment comprises RNA-seq data used to study evolutionary differences between humans and mice in neuronal activity-dependent transcriptional responses. Activity-dependent transcriptional responses in developing human stem cell-derived cortical neurons were compared with those induced in deve...

ORGANISM(S): Mus musculus

2017-02-16 | E-MTAB-5489 | biostudies-arrayexpress

Transcription profiling of rat primary cortical neurons exposed to anesthetics

Inhaled anesthetics produce many effects and bind to a large number of brain proteins, but it is not yet clear if this is accompanied by widespread changes in gene expression of the biological targets. Such changes in expression might implicate functionally important targets from the large pool of ...

ORGANISM(S): Rattus norvegicus

2008-05-07 | E-GEOD-2982 | biostudies-arrayexpress

Slamseq of whole mouse primary cortical neurons (mPCN) with perturbed mRNA degradation machinery

We perturbed mRNA degradation machinery in mouse primary cortical neurons (mPCN) and investigated the change in mRNA half-lives. We performed SLAMseq Metabolic RNA Labeling on Mutant mPCN line harbouring a ponasteroneA-inducible heterozygous dominant-negative Caf1 (dnCaf1) and on GFP-transfected mPC...

ORGANISM(S): Mus musculus

2022-11-14 | E-MTAB-11575 | biostudies-arrayexpress

Global proteome of neurite and soma isolated from primary cortical neurons

Proteome comparison of neurite and soma total protein extracts isolated from mouse cortical neurons.

ORGANISM(S): Mus musculus (Mouse)

2022-11-15 | PXD028300 | Pride

Phactr1/PP1 phosphatase substrates in mouse primary neurons

Neurons express Phactr1 at high level (Allen et al., 2004), and Phactr1 mutations are associated with morphological and functional developmental defects in cortical neurons (Hamada et al., 2018). To identify targets of the Phactr1/PP1 phosphatase holoenzyme, we cultured hippocampal and cortical neur...

ORGANISM(S): Mus musculus (Mouse)

2020-10-28 | PXD019882 | Pride

Neurons Phosphatase Mouse Phactr1

Proteomic analysis of primary cortical neurons in response to acute USP7 loss

A proteomic characterization of primary mouse cortical neurons in response to acute USP7 depletion using 16-plex TMT mass spec

ORGANISM(S): Mus musculus (Mouse)

2025-02-24 | PXD043849 | Pride

Usp7 Cortical neuron

mRNA-seq of neuronal compartments with perturbed mRNA degradation machinery in mouse primary cortical neurons (mPCN)

We have perturbed mRNA degradation machinery and investigated the change in subcellular localization of mRNA in mouse primary cortical neurons (mPCNs). Mutant mPCN line harbouring a ponasteroneA-inducible heterozygous dominant-negative Caf1 (dnCaf1) was generated, separated into neuronal compartment...

ORGANISM(S): Mus musculus

2022-11-14 | E-MTAB-11572 | biostudies-arrayexpress

Global ubiquitylation analysis of mitochondria in primary neurons identifies endogenous Parkin targets following activation of PINK1

Mutations in PINK1 and Parkin lead to Parkinson’s disease. Cell culture-based studies have demonstrated that mitochondrial depolarisation induced by chemical uncouplers can activate PINK1 and Parkin activity. Very little is known on mitochondrial depolarisation signalling in post-mitotic neurons. We...

ORGANISM(S): Mus musculus (Mouse)

2021-09-15 | PXD027614 | Pride

Ubiqutylation Parkinsosn's disease Protoemics Pink1

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