Connectivity - OmicsDI

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Homo sapiens (253)
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bacterioplankton metagenome (2)
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Technology Type

Mass Spectrometry (93)
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Instrument Platform

Liquid Chromatography MS - negative - reverse phase (5)
Liquid Chromatography MS - positive - reverse phase (5)
Illumina NovaSeq 6000 (3)
Illumina HiSeq 4000 (3)
Q Exactive (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)
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GenePix 4000B Microarray Scanner (Molecular Devices). (1)
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TripleTOF 6600 (1)
Liquid Chromatography MS - alternating (1)
Direct infusion MS - negative (1)
Direct infusion MS - positive (1)
Liquid Chromatography MS - (1)
Nuclear Magnetic Resonance (NMR) - (1)
Liquid Chromatography MS - alternating - hilic (1)
Liquid Chromatography MS - positive - reverse-phase (1)

Publication Date

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UNIPROT ID/AC

P05230 (1)
P11362 (1)
P13545 (1)
E2E2U9 (1)
O61230 (1)
Q60821 (1)
P17948 (1)
B0EYG9 (1)
P15056 (1)
P28482 (1)
P04049 (1)

CHEBI ID

CHEBI:17716 (2)
CHEBI:64561 (2)
CHEBI:17822 (2)
CHEBI:26271 (2)
CHEBI:18186 (2)
CHEBI:26986 (2)
CHEBI:16811 (2)
CHEBI:28300 (2)
CHEBI:25017 (2)
CHEBI:28044 (2)
CHEBI:27266 (2)
CHEBI:29016 (2)
CHEBI:15891 (2)
CHEBI:18066 (2)
CHEBI:18132 (2)
CHEBI:16856 (2)
CHEBI:16436 (2)
CHEBI:16264 (2)
CHEBI:17015 (2)
CHEBI:27897 (2)
CHEBI:15354 (2)
CHEBI:90438 (1)
CHEBI:89151 (1)
CHEBI:89366 (1)
CHEBI:89280 (1)
CHEBI:141509 (1)
CHEBI:136122 (1)
CHEBI:167279 (1)
CHEBI:145313 (1)
CHEBI:89415 (1)

Metabolite Name

Adenosine (6)
Citrulline (5)
L-Tryptophan (5)
L-Serine (5)
Creatine (5)
L-Tyrosine (5)
Hypoxanthine (5)
Uracil (4)
Betaine (4)
Lumichrome (4)
L-Histidine (4)
Indole (4)
Taurine (4)
L-Proline (4)
Guanine (4)
Cytosine (4)
Adenine (4)
Xanthine (4)
L-Phenylalanine (4)
Plantamajoside (3)
Prometon (3)
Acetylphosphate (3)
Linoleamide (3)
Hexylamine (3)
Lactose (3)
Heptadecanoic acid (3)
Spermine (3)
Diethanolamine (3)
Kynurenic acid (3)
Homocarnosine (3)

First Public Date

2026 (246)
2025 (204)
2024 (197)
2023 (134)
2022 (118)
2021 (95)
2020 (77)
2019 (68)
2014 (68)
2018 (46)
2017 (39)
2016 (21)
2015 (16)
2013 (15)
2011 (1)

Modelling Approach

Constraint-based model (5)
Ordinary differential equation model (4)

Study status

Terminated (1)
Completed (1)

Lab affiliation

Research Unit Protein Science, Helmholtz Zentrum München (2)
VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium. (2)
1Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, 13 Vienna, Austria (1)
ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France + CIRAD, UMR ASTRE, F-34398, Montpellier, France (1)
Assistant Professor Department of Molecular and Experimental Medicine TSRI - California Campus USA (1)
Assistant Professor Department of Molecular and Experimental Medicine TSRI - California Campus USA (1)
Basic Immune System of Plants / Protein Mass Spectrometry Max Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10, 50829 Cologne, Germany (1)
Basilbiotech, Incheon 22002, Republic of Korea. (1)
Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile Center for Geroscience, Brain Health and Metabolism, Santiago, Chile Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile Buck Institute for Research on Aging, Novato, CA, USA (1)
Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile. Center for Geroscience, Brain Health and Metabolism, Santiago, Chile. Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile. (1)
Center for Neurogenomics and Cognitive Research, VU Amsterdam De Boelelaan 1085 1081 HV Amsterdam (1)
Center for Neuroscience Research, Children's National Hospital, Washington, DC. 20010 USA (1)
Clinical Proteomics Mass Spectrometry, Science for Life Laboratory, Dept. of Oncology Pathology, Karolinska Institutet (1)
Core Facility Proteomics, Department of Clinical Chemistry, University Medical Center Göttingen, Germany (1)
Core Unit Proteomics, Berlin Institute of Health at Charite - Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine, Berlin, Germany (1)
Department of Biochemistry and Biomedical Sciences McMaster University (1)
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, United States (1)
Department of Biology, Stanford University, Stanford, CA, 94305 (1)
Department of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan Taiwan (1)
Department of Chemistry and Biochemistry, Texas Tech University (1)
Department of Chemistry, Durham University, Stockton Rd, DH1 3LE, Durham, United Kingdom (1)
Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States (1)
Department of Dental Implant Center, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China (1)
Department of Dermatology, Stanford School of Medicine, Stanford University (1)
Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy (1)
Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia (1)
Department of Molecular and Cellular Neurobiology, Center for Neurogenomics & Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands (1)
Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, The Netherlands (1)
Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Norway (1)
Department of Ophthalmology, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin, Korea (1)

Keyword

PTSD (1)
Memory Structuring Intervention (MSI) (1)
Vagal breathing (1)

IsPrivate

False (11)

Model Flag

Non Kinetic (5)

Submitter Keywords

FROG (2)
Not Peer Reviewed (1)

Classification

viruses (3)
bacteria (3)
fungi (1)
protozoa (1)

Modification

4-tetrahydrothiazine-3-carboxylic acid (1)

Study type

Transcription profiling by array (112)
Unknown experiment type (28)
RNA-seq of coding RNA (23)
ChIP-seq (9)
Other (4)
RNA-seq of coding RNA from single cells (4)
Methylation profiling by array (3)
Transcription profiling by SAGE (1)
ChIP-chip by tiling array (1)
Human - One-color microarray (1)
Transcription profiling by RT-PCR (1)
Comparative genomic hybridization by array (1)
RNA-seq of total RNA (1)
Observational (1)
Interventional (1)

Release Date

2025 (3174)
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2010 (235)
2009 (153)
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2007 (86)
2006 (51)
2005 (24)
2004 (17)
2003 (11)
2002 (10)
2001 (6)
1996 (2)
2000 (1)
1998 (1)

Location

France (1)
United States (1)

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Reduced ER-mitochondria connectivity promotes neuroblastoma multidrug resistance

Not available

ORGANISM(S): Homo sapiens

ST002054 | MetabolomicsWorkbench

Excessive local host-graft connectivity in aged and amyloid-loaded brain

Transplantation is a clinically relevant approach for brain repair, but much remains to be understood about influences of the disease environment in the host on transplant connectivity. To explore the influence of ageing and amyloid pathology in Alzheimer's disease (AD) we examined graft connectivit...

ORGANISM(S): Mus musculus (Mouse)

2022-08-12 | PXD023407 | Pride

A clinically applicable connectivity signature for glioblastoma includes the tumor network driver CHI3L1

Tumor microtubes (TMs) connect glioma cells to a network with considerable relevance for tumor progression and therapy resistance. The determination of TM-interconnectivity in individual tumors has been challenging and the impact on patient survival unresolved. Here, a connectivity signature from si...

ORGANISM(S): Homo sapiens (Human)

2023-11-27 | PXD044001 | Pride

Gene expression signature Glioblastoma Connectivity Tumor microtubes Single-cell rna-sequencing

Geodia hentscheli connectivity and adaptation

PRJEB85623 | ENA

Migration connectivity of Rook in Korea

PRJEB102121 | ENA

Promoter Decommissioning by the NuRD Chromatin Remodeling Complex Triggers Synaptic Connectivity in the Mammalian Brain

Precise control of gene expression plays fundamental roles in brain development, but the roles of chromatin regulators in neuronal connectivity have remained poorly understood. Here, we find that depletion of the nucleosome remodeling and deacetylation (NuRD) complex in the cerebellar cortex by in v...

ORGANISM(S): Mus musculus

2014-08-18 | E-GEOD-57758 | biostudies-arrayexpress

HDL Quality Features Revealed by Proteome-Lipidome Connectivity are Associated with Atherosclerotic Disease

The “quality” rather than “quantity” of lipoprotein particles is more relevant to cardiovascular diseases (CVD), since lipoprotein particles are highly heterogeneous. However, the targeted separation, detection, and exploration of the heterogeneous on omic-scale for lipoprotein remain challenging an...

ORGANISM(S): Homo Sapiens

2020-02-15 | PXD017529 |

Detecting Functional Connectivity During Audiovisual Integration with MEG: A Comparison of Connectivity Metrics.

Not available

S-EPMC4533088 | biostudies-literature

Bulk RNA sequencing of high- and low-functional connectivity glioblastomas

PRJNA924786 | ENA

Effects of connectivity history on fungal community dynamics and recovery

PRJEB112528 | ENA

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