de Jong S S - OmicsDI

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Unknown (1444)
Transcriptomics (95)
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Homo sapiens (64)
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46170 (1)
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Organisms

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Repository

biostudies-arrayexpress (101)
pride (39)
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Disease

Plasmodium falciparum malaria (2)
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Technology Type

Mass Spectrometry (39)
Shotgun proteomics (20)
Bottom-up proteomics (11)
Data-dependent acquisition (4)
Mass spectrometry (3)
Top-down proteomics (2)
Affinity purification coupled with mass spectrometry proteomics (1)
All-ion fragmentation (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)
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Instrument Platform

Illumina NovaSeq 6000 (7)
Illumina HiSeq 2000 (3)
LTQ FT (2)
NextSeq 550 (1)
Illumina HiSeq 4000 (1)
LCMS-9030 (1)
LTQ (1)
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Shimadzu Nexera X2 UHPLC system, with attached PDA, coupled to Shimadzu 9030 QTOF mass spectrometer, standard ESI source (1)
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LTQ Orbitrap (1)

Publication Date

2014 (16)
2008 (16)
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2012 (12)
2025 (11)
2013 (11)
2010 (10)
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2016 (8)
2024 (5)
2026 (5)
2018 (5)
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2017 (3)
2011 (3)
2009 (3)
2007 (3)
2019 (2)
2006 (1)

CHEBI ID

CHEBI:15741 (2)
CHEBI:16196 (2)
CHEBI:16359 (2)
CHEBI:16811 (2)
CHEBI:17351 (2)
CHEBI:17754 (2)
CHEBI:17822 (2)
CHEBI:17992 (2)
CHEBI:18222 (2)
CHEBI:22653 (2)
CHEBI:24898 (2)
CHEBI:25017 (2)
CHEBI:26271 (2)
CHEBI:26986 (2)
CHEBI:27266 (2)
CHEBI:27897 (2)
CHEBI:28044 (2)
CHEBI:28757 (2)
CHEBI:28834 (2)
CHEBI:28865 (2)
CHEBI:32816 (2)
CHEBI:33508 (2)
CHEBI:37684 (2)
CHEBI:6650 (2)
CHEBI:75342 (2)
CHEBI:9410 (2)
CHEBI: (1)
CHEBI:10213 (1)
CHEBI:10352 (1)
CHEBI:133077 (1)

Metabolite Name

Asparagine (2)
Fructose (2)
Glyceric acid (2)
Glycerol (2)
Isoleucine (2)
Leucine (2)
Malic acid (2)
Mannose (2)
Methionine (2)
Phenylalanine (2)
Proline (2)
Pyruvic acid (2)
Serine (2)
Succinic acid (2)
Sucrose (2)
Threonine (2)
Tryptophan (2)
Valine (2)
Xylose (2)
4-Aminobutyric acid (1)
Alanine (1)
Arginine (1)
Aspartic acid (1)
Cholic acid (1)
Citric acid (1)
Cyclic-Lysophosphatidic acid (14:0) (1)
Cyclic-Lysophosphatidic acid (16:1) (1)
Cyclic-Lysophosphatidic acid (18:0) (1)
Cyclic-Lysophosphatidic acid (18:1) (1)
Cyclic-Lysophosphatidic acid (18:2) (1)

IsPrivate

False (1)

First Public Date

2014 (3)
2025 (1)
2015 (1)
2013 (1)

Modelling Approach

Logical model (1)

Modification

15.994915 (1)
42.010565 (1)
57.021464 (1)
79.966331 (1)

Study type

Transcription profiling by array (64)
RNA-seq of coding RNA (8)
Comparative genomic hybridization by array (7)
ChIP-seq (4)
RNA-seq of coding RNA from single cells (3)
Other (2)
Methylation profiling by array (2)
Methylation profiling by high throughput sequencing (2)
Transcription profiling by SAGE (1)
Unknown experiment type (1)
Human - Single-cell sequencing (1)
Human - High-throughput sequencing (1)
ChIP-chip by array (1)
Spatial transcriptomics by high-throughput sequencing (1)
Single nucleus RNA sequencing (1)
RNA-seq of total RNA (1)
RNA-seq of non coding RNA (1)

Release Date

2022 (165)
2025 (162)
2021 (150)
2023 (146)
2020 (115)
2024 (113)
2019 (104)
2017 (87)
2016 (75)
2015 (66)
2014 (66)
2018 (65)
2012 (40)
2013 (34)
2010 (30)
2026 (28)
2008 (28)
2011 (25)
2009 (13)
2007 (11)
2006 (10)
2005 (4)
2004 (3)
2003 (2)
2001 (2)
2002 (1)

Lab affiliation

University of Greifswald, Institute of Microbiology, Department of Microbial Proteomics, Greifswald, Germany (2)
biomolecular mass spectrometry (2)
Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands (1)
Assistant professor, School of Biological Sciences, Seoul National University (1)
Associate Professor Microbiology and Immunology Department Upstate Medical University Weiskotten Hall Rm. 2273 766 Irving Avenue Syracuse, NY 13210 Tel 315.464.5870 (1)
BMBB, University of Minnesota, USA (1)
Biomolecular Mass Spectrometry and Proteomics (1)
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands; and Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. (1)
Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada (1)
Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea School of Biological Sciences, Seoul National University, Seoul 08826, Korea (1)
Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA (1)
Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. (1)
Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany (1)
Department of Molecular Physiology, Leiden University & Oncode Institute, Leiden 2333 CC, Netherlands (1)
Dr. Andreas Otto Institute for Microbiology Department of Microbial Proteomics Ernst-Moritz-Arndt-University Greifswald F.-L.-Jahn-Str. 15 17489 Greifswald phone: +49 3834 4205920 fax: +49 3834 4205902 (1)
EDyP (1)
Facultad de Estudios Superiores Iztacala, Unidad de Biomedicina, Universidad Nacional Autónoma de México, México (1)
Faculty of Science (1)
Head Proteomics Group Leiden University Medical Center, Center for Proteomics and Metabolomics, PO Box 9600, Postal zone P1-Q, 2300 RC Leiden, The Netherlands (1)
Head Proteomics Group , Leiden University Medical Center, Center for Proteomics and Metabolomics, PO Box 9600, Postal zone P1-Q, 2300 RC Leiden, The Netherlands (1)
Head Proteomics Group, Leiden University Medical Center, Center for Proteomics and Metabolomics, PO Box 9600, Postal zone P1-Q, 2300 RC Leiden, The Netherlands (1)
Institute for Microbiology Department of Microbial Proteomics Ernst-Moritz-Arndt-University Greifswald F.-L.-Jahn-Str. 15 17489 Greifswald phone: +49 3834 864073 fax: +49 3834 864202 (1)
Institute for Microbiology Department of Microbial Proteomics and Mass Spectrometry Ernst-Moritz-Arndt-University Greifswald F.-L.-Jahn-Str. 15 17489 Greifswald phone: ++49 3834 864073 ++49 3834 864072 (1)
Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany (1)
Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA. (1)
Mass spectrometry of Biomacromolecules, SILS, Universiteit van Amsterdam, The Netherlands (1)
Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands. & Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, The Netherlands. (1)
Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands. (1)
SUNY Upstate Medical University, Department of Biochemistry and Molecular Biology (1)
School of Biomedical and Healthcare Sciences Plymouth University Peninsula Schools of Medicine and Dentistry Plymouth University (UK) (1)

Tags

xref:PubMed:24887064 (3)
xref:PubMed:26173112 (1)
xref:PubMed:30739914 (1)

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Exoproteomes of S. aureus spa type t437 isolates

A total of 20 S. aureus spa type t437 isolates were used for exoproteome analyses in the present study. Ten of them were selected from MLVA type (MT) 621 group which has was shown to represent the most predominant class of S. aureus isolates with the spa type t437; the other ten isolates belonged to...

ORGANISM(S): Staphylococcus aureus

2019-05-24 | PXD009082 | Pride

Staphylococcus aureus

Transcription profiling of S. cerevisiae during prolonged maltose limited cultivation

Prolonged cultivation (>25 generations) of Saccharomyces cerevisiae in aerobic, maltose-limited chemostat cultures led to profound physiological changes. Maltose hypersensitivity was observed when cells from prolonged cultivations were suddenly exposed to excess maltose. This substrate hypersensitiv...

ORGANISM(S): Saccharomyces cerevisiae

2008-06-16 | E-GEOD-8897 | biostudies-arrayexpress

The response of Streptococcus pneumoniae to replication stress on the transcriptome of a wild-type strain

The aim of this study is to identify the response of S. pneumoniae to HPUra-induced replication stress on transcriptional level in a wild type strain. Two cultures were compared to each other. One treated with HPUra and one untreated. A dye-swap was included, and both the dye-swap and original label...

ORGANISM(S): Streptococcus pneumoniae D39

2013-04-23 | E-GEOD-46002 | biostudies-arrayexpress

Mito-phylogenetic relationship of the new subspecies of gentle monkey Cercopithecus mitis manyaraensis, Butynski & De Jong, 2020.

Not available

S-EPMC9285482 | biostudies-literature

Transcription profiling of S. cerevisiae to investigate formaldehyde as source of free-energy during growth on glucose

Previously, it has been demonstrated that formate can be utilized by Saccharomyces cerevisiae as additional energy source using cells grown in a glucose-limited chemostat. Here, we investigated utilization of formaldehyde as co-substrate. Since endogenous formaldehyde dehydrogenase activities were i...

ORGANISM(S): Saccharomyces cerevisiae

2008-10-18 | E-GEOD-8902 | biostudies-arrayexpress

Psychometric Properties of the 11-Item De Jong Gierveld Loneliness Scale in a Representative Sample of Mexican Older Adults.

Not available

S-EPMC9957099 | biostudies-literature

Transcription profiling of S. cerevisiae grown in acetate, ethanol and maltose limited conditions to investigate transcriptional regulation in controlling fluxes in central carbon metabolism

In contrast to batch cultivation, chemostat cultivation allows the identification of carbon source responses without interference by carbon-catabolite repression, accumulation of toxic products, and differences in specific growth rate. This study focuses on the yeast Saccharomyces cerevisiae, grown ...

ORGANISM(S): Saccharomyces cerevisiae

2008-06-16 | E-GEOD-8895 | biostudies-arrayexpress

Protein S-Nitrosylation of host and viral proteins upon fibroblast infection with Human Cytomegalovirus

Human Cytomegalovirus (HCMV) is a ubiquitous pathogen that has co-evolved with its host and in doing so, is highly efficient in undermining antiviral responses that limit successful infections. As a result, HCMV infections are highly problematic in individuals with weakened or underdeveloped immune ...

ORGANISM(S): Homo sapiens (Human)

2020-07-03 | PXD019208 | Pride

Hcmv Protein s-nitrosylation Cytomegalovirus

Taxonomic notes on the genus <i>Spinosodus</i> Breuning & de Jong, 1941 (Coleoptera, Cerambycidae) with a generic and specific synonym.

Not available

S-EPMC11759920 | biostudies-literature

Transcription profiling of S. cerevisiae after prolonged selection in aerobic, glucose-limited chemostat cultures

Prolonged cultivation of Saccharomyces cerevisiae in aerobic, glucose-limited chemostat cultures (dilution rate, 0Â·10 hâ€“1) resulted in a progressive decrease of the residual glucose concentration (from 20 to 8 mg lâ€“1 after 200 generations). This increase in the affinity for glucose was accompan...

ORGANISM(S): Saccharomyces cerevisiae

2008-06-16 | E-GEOD-8898 | biostudies-arrayexpress

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