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NucleoSpin RNA/Protein kit lysis buffer (350 µL per tube; Macherey‑Nagel). (6)
Dell PowerEdge R750; CPU: 2 × Intel Xeon Gold 6346 (32 Cores / 64 Threads); RAM: 188 GB (6)
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See manuscript (5)
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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)
FastPrep‑24 homogenizer (MP Biomedicals), operated at 5 m/s for 10 seconds. (2)
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CHEBI ID

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Metabolite Name

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IsPrivate

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First Public Date

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Classification

bacteria (11)
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Modelling Approach

Differential equation model (1)

Modification

N6 (2)
+3amu) (1)
-17.026549 (1)
-18.010565 (1)
15.994915 (1)
4-tetrahydrothiazine-3-carboxylic acid (1)
42.010565 (1)
4x(2)H labeled dimethylated residue (1)
57.021464 (1)
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Lab affiliation

EDyP (4)
GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Avenida Lineu Prestes 1374, CEP 05508-000, Sao Paulo, Brazil (3)
University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry (3)
Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee (2)
Chair of Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany (2)
Department of Agronomy Iowa State University (2)
Department of Biology – Cellular Proteostasis and Mass Spectrometry, University of Konstanz (2)
Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy (2)
Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany (2)
Mass Spectrometry Facility, Max Perutz Labs Vienna, University of Vienna, Vienna Biocenter, Dr.-Bohr-Gasse 7, 1030 Vienna (2)
Molecular Genetics, RPTU Kaiserslautern, Germany (2)
Molecular Physiology & Biophysics, Wright Lab, University of Iowa, USA (2)
Peking University (2)
Proteomic Platform, Laboratory of Molecular Parasitology, Université Libre de Bruxelles, Belgium (2)
University Clinic for Poultry and Fish Medicine, University of Veterinary Medicine, Vienna, Austria (2)
1 Biochemistry & Microbiology, University of Victoria, Victoria, BC, Canada 2 Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada (1)
1) Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany 2) Department of Microbiology and Molecular Biology, Friedrich Schiller University, Jena, Germany (1)
1. Centre for Gene Therapy and Regenerative Medicine, King’s College London, London, UK 2. Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany (1)
1. Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 2. Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan (1)
1.School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong 3216, Australia 2.Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, 3168 Melbourne, Australia 3.Department of Molecular and Translational Science, Monash University, 3168 Melbourne, Australia (1)
1Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain (1)
1Nutrient Metabolism & Signalling Laboratory, Metabolism, Diabetes and Obesity Program, Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia. 2Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Faculty of Medicine, Nursing & Health Sciences, Monash University, Victoria 3800, Australia. (1)
225, Veterinary Medical Center University of Minnesota 1365, Gortner Avenue St. Paul, MN 55108 (1)
2Departments of Internal Medicine, University of Michigan, Ann Arbor MI 48109, USA. (1)
Assistant Professor, Pediatrics-Heme/Onc and Bone Marrow Transplantation (1)
Assistant professor, School of Biological Sciences, Seoul National University (1)
Associate Professor, Department of Biochemistry & Molecular Biology, UTMB Mass Spectrometry Director, University of Texas Medical Branch – Galveston, Texas, USA (1)
Associate Professor, University College Dublin, School of Biomolecular and Biomedical Science, Conway Institute Belfield Dublin 4 (1)
Augusta University Medical College of Georgia (1)
BK21 Plus KNU Multi-Omics-based Creative Drug Research Team, College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Republic of Korea (1)

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Characterization of Campylobacter jejuni proteome profiles in co-incubation scenarios

This study aimed to reveal the influence of co-incubation with Enterococcus faecalis, Enterococcus faecium, or Staphylococcus aureus on the proteome of C. jejuni 81–176 using data-independent-acquisition mass spectrometry (DIA-MS). We compared the proteome profiles during co-incubation with the prot...

ORGANISM(S): Campylobacter jejuni subsp. jejuni 81-176

2023-11-02 | PXD046477 | Pride

Gene expression data from NK cells sorted for PD-L1 after co-incubation with K562 myeloid leukemia cells

PRJNA549615 | ENA

Characterization of Campylobacter jejuni proteome profiles in co-incubation scenarios.

Not available

S-EPMC10666060 | biostudies-literature

Gene expression data from NK cells sorted for PD-L1 after co-incubation with K562 myeloid leukemia cells

The objective was to determine if there are differences in gene expression in PD-L1+ and PD-L1- NK cells after co-incubation of NK cells with target K562 myeloid leukemia cells.

ORGANISM(S): Homo sapiens

2019-10-18 | GSE132976 | GEO

Does reducing gamete co-incubation time improve clinical outcomes: a retrospective study.

Not available

S-EPMC4717136 | biostudies-literature

GNPS - HNRC samples co-analyzed with drug microbial incubation (MSV000095331)

HNRC samples co-analyzed with drug microbial incubation (MSV000095331) for retention time matching with drug microbial metabolites

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

2024-10-02 | MSV000096012 | GNPS

Co-Incubation with PPARβ/δ Agonists and Antagonists Modeled Using Computational Chemistry: Effect on LPS Induced Inflammatory Markers in Pulmonary Artery.

Not available

S-EPMC8003823 | biostudies-literature