Neuron culture - OmicsDI

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Repository

biostudies-arrayexpress (594)
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Cell culture (149)
Brain (39)
Neuron (34)
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Primary cell (8)
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Neuron of cerebral cortex (6)
Astrocyte (6)
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Generation of neurons (2)
Astrocyte of the cerebral cortex (2)
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Technology Type

Mass Spectrometry (195)
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ILLUMINA, Illumina HiSeq 2500 (1)
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Chemical cross-linking coupled with mass spectrometry proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (66)
NextSeq 500 (21)
Illumina HiSeq 2500 (19)
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NextSeq 550 (9)
Illumina HiSeq 2000 (9)
Illumina HiSeq 3000 (4)
Qubit 4.0 Fluorometer/ Agilen 5300 Fragment Analyzer (3)
PromethION (3)
Illumina NovaSeq X (3)
NA (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)
Sequel IIe (2)
Sony SH800 (2)
Agilent G2565AA and G2565BA Microarray Scanner (2)
Scanning hardware (2)
NextSeq 2000 (2)
Illumina HiSeq 1500 (2)
Bravo automated liquid handling robot station (Agilent) (1)
RiboErase Roche (1)
Qiagen RNaesy kit (1)
STAR v2.5.3a, rpkmforgenes, RSeQC 2.6.1 (1)
Illumina Nextera XT index kits (Set A–D) (1)
Oligo(dT) primer and SuperScript II reverse transcriptase (ThermoFisher Scientific), TapeStation 4200 or 2100 Bioanalyzer with a DNA High Sensitivity chip (Agilent Biotechnologies) (1)
Aria III (BD Biosciences) (1)
Python (1)
Nugen Ovation SPIA; Wafergen’s Apollo liquid handler; KAPA Hyper Prep Library Kit (1)
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Isoflurane euthanasia chamber (1)
Chromium Next GEM Chip G (1)

Publication Date

2025 (90)
2026 (79)
2014 (75)
2013 (64)
2015 (62)
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2012 (54)
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2016 (45)
2020 (43)
2011 (39)
2024 (38)
2008 (33)
2017 (30)
2010 (29)
2018 (26)
2009 (20)
2007 (18)
2019 (16)
2006 (9)
2005 (4)
2003 (1)
2004 (1)

CHEBI ID

CHEBI:73688 (2)
CHEBI:16668 (2)
CHEBI:193326 (1)
CHEBI:2756 (1)
CHEBI:175933 (1)
CHEBI:181116 (1)
CHEBI:167992 (1)
CHEBI:184039 (1)
CHEBI:181285 (1)
CHEBI:181855 (1)
CHEBI:182145 (1)
CHEBI:182866 (1)
CHEBI:40036 (1)
CHEBI:125539 (1)
CHEBI:182487 (1)
CHEBI:181736 (1)
CHEBI:53785 (1)
CHEBI:182213 (1)
CHEBI:93826 (1)
CHEBI:3044 (1)
CHEBI:92338 (1)
CHEBI:3104 (1)
CHEBI:109547 (1)
CHEBI:81217 (1)
CHEBI:31460 (1)
CHEBI:4402 (1)
CHEBI:135010 (1)
CHEBI:176310 (1)
CHEBI:188660 (1)
CHEBI:181654 (1)

Metabolite Name

Isopentenyladenine (2)
LPE 18:2 (2)
Catechin (2)
LPC 16:0 (2)
N-Acetyl-L-phenylalanine (2)
(+-)-Baclofen (1)
(3E)-3-Benzylidene-4-Methyl-1H-1,4-Benzodiazepine-2,5-Dione (1)
(5R)-5-Hydroxy-1-(4-Hydroxy-3-Methoxyphenyl)Tetradecan-3-One (1)
1,2-Dihydroxyheptadec-16-En-4-Yl Acetate (1)
2,5-Dihydroxy-3-Undecylcyclohexa-2,5-Diene-1,4-Dione (1)
2-Naphthalene Sulfonic Acid (1)
3-Deoxysappanchalcone (1)
3-Indoxyl Sulfate (1)
3-Phospho-D-Glycerate (1)
3-Sulfino-L-Alanine (1)
4,4`-Thiodiphenol (1)
4-Methylumbelliferyl Sulfate (1)
5,10-Dimethoxy-2,2-Dimethylpyrano[3,2-G]Chromen-8-One (1)
5,7-Dihydroxy-2-(4-Hydroxyphenyl)-3-Methoxy-4H-Chromen-4-One (1)
5,7-Dihydroxy-6-Methoxy-2-Phenylchromen-4-One (1)
5-Chlorodivaricatinic Acid (1)
Adenosine-3-Monophosphate (1)
Alpha-D-(+)-Mannose 1-Phosphate (1)
Alpha-D-Glucose-1,6-Diphosphate (1)
Alternariol Monomethyl Ether (1)
Beta-Hydroxymyristic Acid (1)
Bisphenol S (BPS) (1)
C12-AS (1)
Chlorothalonil-4-Hydroxy (1)
D-(+)-Pantothenic Acid (1)

First Public Date

2025 (45)
2026 (27)
2024 (24)
2022 (22)
2014 (22)
2023 (20)
2020 (19)
2021 (11)
2017 (10)
2018 (9)
2019 (5)
2015 (5)
2013 (3)
2016 (1)

Modification

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

Study type

Transcription profiling by array (315)
RNA-seq of coding RNA (139)
RNA-seq of coding RNA from single cells (48)
ChIP-seq (31)
RNA-seq of total RNA (9)
Methylation profiling by high throughput sequencing (8)
Methylation profiling by array (5)
Cell line - High-throughput sequencing (4)
Comparative genomic hybridization by array (4)
Other (4)
Cell line - Single-cell sequencing (3)
ATAC-seq (3)
Transcription profiling by SAGE (2)
Differential (2)
ChIP-chip by tiling array (2)
Cell line - One-color microarray (2)
Single nucleus RNA sequencing (2)
Animal - One-color microarray (1)
Human - Single-cell sequencing (1)
Translation profiling (1)
Animal - High-throughput sequencing (1)
Transcription profiling by tiling array (1)
Genotyping by array (1)
Capture-C (1)
Transcription profiling by RT-PCR (1)
MicroRNA profiling by array (1)
DNA-seq (1)

Release Date

2021 (113)
2025 (112)
2022 (110)
2014 (109)
2023 (104)
2020 (94)
2015 (87)
2016 (85)
2013 (83)
2012 (77)
2018 (75)
2024 (71)
2019 (70)
2017 (64)
2011 (51)
2010 (44)
2008 (41)
2026 (40)
2009 (31)
2007 (20)
2006 (13)
2005 (4)
2002 (4)
2001 (4)
2003 (3)
2004 (1)
1997 (1)

Lab affiliation

UMR 7367 CNRS-UL IMoPA Biopôle de l'Université de Lorraine Campus Brabois-Santé 9 avenue de la forêt de Haye 54505 Vandoeuvre-les-Nancy FRANCE (4)
UCSF (4)
School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China (2)
Howard Hughes Medical Institute NYU School of Medicine-Smilow Research Center Biochemistry Department (2)
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, the Netherlands. (2)
DZNE Munich Neuroproteomics Feodor-Lynen-Str. 17 81377 Munich Germany (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)
DZNE Munich, Neuroproteomics, Feodor-Lynen-Str. 17, 81377 München, Germany (2)
Developmental Neurobiology, Max Planck Institute of Psychiatry, Munich, Germany (1)
Northwestern University Feinberg School of Medicine (1)
Cambridge Centre for Proteomics University of Cambridge (1)
Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany (1)
Max Planck Institute of Psychiatry, Munich, Germany Biomedical Center, Molecular Biology, Ludwig-Maximilians-Universitat, Munich, Germany (1)
Associate Professor, Department of Neurology, Yale University School of Medicine (1)
Dominick P. Purpura Department of Neuroscience, Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA (1)
Massachusetts General Hospital, USA (1)
The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK (1)
The Solomon H. Snyder Department of Neuroscience Johns Hopkins University School of Medicine USA (1)
Ruhr-University Bochum Medizinisches Proteom-Center Clinical Proteomics (1)
Synapse Proteomics Group, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia (1)
Department of Clinical Research, University of Bern (1)
Organic Mass Spectrometry Laboratory, Department of Chemical Sciences, University of Catania, Via S. Sofia 64, 95123 Catania, Italy (1)
Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA (1)
MPI for Brain Research, Proteomics, Frankfurt, Germany (1)
University of Pennsylvania, Cell and Developmental Biology, Epigenetics Institute (1)
Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women’s and Children’s Health, Karolinska Institute, Region Stockholm, Stockholm, Sweden Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden (1)
Queensland Brain Institute, Univerisity of Queensland (1)
Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Germany (1)
Group Leader Proteostasis Charité Universitätsmedizin Berlin, Germany (1)

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A microfluidic co-culture platform to generate synaptically separated networks that uncover the role of astrocytes in the initiation and progression of neuron pathology

Communication between astrocytes and neurons plays a pivotal role in the development, maintenance and dysfunction of cellular networks within the central nervous system. Further understanding the contribution of astrocytes to the initiation and progression of neuropathology has, however, been hinder...

ORGANISM(S): Rattus norvegicus (Rat)

2026-06-08 | PXD055523 | Pride

Identification of genes expressed with temporal-spatial restriction to developing cerebellar neuron precursors by a functional genomic approach perspective of human cancers.

Swiss-Webster B mouse postnatal day 4-5 primary cerebellar culture (pooled from litter mates) treated with sonic hedgehog (Shh), controls (veh), growth arrested (arrest), cycloheximide (cyc) for 1, 3 and 24 hours. Different treatment conditions with biological replicates. Mouse cerebellar granule ce...

ORGANISM(S): Mus musculus

2013-09-06 | E-GEOD-50606 | biostudies-arrayexpress

Effects of human skeletal muscle fibroblast and stem cell media on cultured rat motor neuron cells

The study was designed to compare whether and how muscle fibroblasts (FIB) and muscle stem cells (MYO) interact with motor neurons. Moreover, we aimed to investigate whether muscle cells, isolated from lifelong exercisers, exerted a protective and supportive effect on motor neurons. These object...

ORGANISM(S): Rattus norvegicus

2026-02-21 | E-MTAB-14399 | biostudies-arrayexpress

1,25-dihydroxyvitamin D3-induced genes in mouse mixed neuron-glial cell cultures

Transcriptomic response of mouse mixed neuron-glial cell cultures to 1,25-dihydroxyvitamin D3 6 samples are analysed with three biological replicates in two conditions, control versus 1,25-dihydroxyvitamin D3 (1,25(OH)2D3)

ORGANISM(S): Mus musculus

2013-03-25 | E-GEOD-41184 | biostudies-arrayexpress

A SUMOylated C-terminus fragment of glutamate transporter EAAT2 linked to inherited ALS mediates motor axon impairment

Downregulation of expression and activity levels of the astroglial glutamate transporter EAAT2 is thought to be implicated in motor neuron excitotoxicity in amyotrophic lateral sclerosis (ALS). We previously reported that EAAT2 is cleaved by caspase-3 at the cytosolic C-terminus domain, impairing th...

ORGANISM(S): Mus musculus

2011-07-19 | E-GEOD-26070 | biostudies-arrayexpress

An intricate interplay between astrocytes and motor neurons in ALS

Amyotrophic Lateral Sclerosis (ALS) results from the selective and progressive degeneration of motor neurons. Although the underlying disease mechanisms remain unknown, glial cells have been implicated in ALS disease progression. Here we examine the effects of glial cell/motor neuron interactions on...

ORGANISM(S): Mus musculus

2013-02-11 | E-GEOD-43879 | biostudies-arrayexpress

Pathways Disrupted in Human ALS Motor Neurons Identified Through Genetic Correction of Mutant SOD1

Although many distinct mutations in a variety of genes are known to cause Amyotrophic Lateral Sclerosis (ALS), it remains poorly understood how they selectively impact motor neuron biology and whether they converge on common pathways to cause neural degeneration. Here, we have combined reprogramming...

ORGANISM(S): Homo sapiens

2014-02-03 | E-GEOD-54409 | biostudies-arrayexpress

RNA-Seq of GNRH1 neurons differentiated from human pluripotent stem cells

This experiment was conducted to identify the transcriptome of human GNRH1 cells which has never been reported before and this experiment has identified some novel molecules which might regulate GNRH1 neuron differentiation which could be further explored to identify the origin and development of...

ORGANISM(S): Homo sapiens

2020-02-16 | E-MTAB-7938 | biostudies-arrayexpress

RNA-Seq of GNRH1 neurons differentiated from human pluripotent stem cells (2)

ORGANISM(S): Homo sapiens

2020-02-16 | E-MTAB-7956 | biostudies-arrayexpress

Human skeletal muscle fibroblasts and stem cells cultured with rat motor neuron cells

ORGANISM(S): Homo sapiens

2026-02-21 | E-MTAB-14395 | biostudies-arrayexpress

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