Yersinia - OmicsDI

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Unknown (2014)
Genomics (1010)
Transcriptomics (310)
Proteomics (60)
Metabolomics (8)
Other (6)
Models (2)
Methylation profiling (1)

Organisms

Yersinia pestis (95)
Homo sapiens (54)
Yersinia pseudotuberculosis (38)
Mus musculus (37)
Yersinia pseudotuberculosis YPIII (16)
Yersinia enterocolitica (15)
Yersinia pseudotuberculosis IP 32953 (12)
Tetranychus urticae (6)
Rattus norvegicus (5)
Malus domestica (4)
Helicoverpa armigera (4)
Oryza sativa (4)
Salmo salar (4)
Candidatus Phytoplasma asteris (3)
Spodoptera frugiperda (3)
Bos taurus (3)
Anopheles merus (3)
Yersinia enterocolitica subsp. palearctica Y11 (3)
Cimex lectularius (2)
Haematobia irritans (2)
Bemisia tabaci (2)
Locusta migratoria (2)
Vitis vinifera (2)
Anopheles gambiae (2)
Apodemus sylvaticus (2)
Yersinia intermedia ATCC 29909 (2)
Saccharomyces cerevisiae S288C (1)
Diabrotica virgifera virgifera (1)
Spodoptera exigua (1)
Plutella xylostella (1)

Organisms

Yersinia pestis (190)
Yersinia enterocolitica (72)
Yersinia pseudotuberculosis (65)
Yersinia ruckeri (27)
Mus musculus (21)
Yersinia (12)
Yersinia pseudotuberculosis YPIII (10)
Homo sapiens (10)
Yersinia pseudotuberculosis IP 32953 (8)
Yersinia pestis subsp. pestis (8)
Yersinia kristensenii (6)
Yersinia wautersii (6)
Yersinia enterocolitica subsp. palearctica (5)
Yersinia pestis CO92 (5)
Yersinia enterocolitica subsp. enterocolitica (5)
Yersinia entomophaga (4)
Yersinia intermedia (3)
Yersinia pestis EV76-CN (3)
Yersinia rochesterensis (3)
Xenopsylla cheopis (3)
Yersinia enterocolitica subsp. palearctica Y11 (2)
Yersinia massiliensis (2)
Yersinia pestis Antiqua (2)
Yersinia pestis KIM10+ (2)
Yersinia pestis INS (2)
Yersinia rohdei (2)
Yersinia pestis Angola (2)
Yersinia pestis Nepal516 (2)
Yersinia pseudotuberculosis str. PA3606 (2)
Yersinia pestis str. Pestoides B (2)

Repository

ENA (981)
biostudies-arrayexpress (193)
geo (145)
pride (34)
iProX (13)
EVA (12)
MassIVE (10)
MetaboLights (8)
BioModels (2)
EGA (1)

Tissue

Cell culture (2)
Blood (1)
Bone marrow (1)
Dental pulp (1)
Epithelial cell (1)
Kidney (1)
Macrophage (1)
Small intestine mucosa (1)
Spleen (1)

Disease

Hepatocellular carcinoma (2)
Yersinia enterocolitica uninfected (1)
Yersinia enterocolitica WAP infected (virulent) (1)
Normal (1)
Breast cancer (1)
Neuroblastoma (1)
Yersinia enterocolitica intestinal infectious disease (1)

Technology Type

Mass Spectrometry (34)
Shotgun proteomics (19)
Bottom-up proteomics (12)
Mass spectrometry (7)
Data-dependent acquisition (2)
Gel-based experiment (2)
Mass spectrometry assay (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)

Instrument Platform

Illumina HiSeq 2000 (16)
NextSeq 500 (8)
Variable Atmosphere Incubator (3)
Illumina HiSeq 2500 (3)
Q Exactive Plus (3)
Axon GenePix4000B (2)
GenePix 4000B [Axon Instruments] (2)
Illumina NovaSeq X (2)
NextSeq 550 (2)
Illumina HiSeq 4000 (2)
LTQ (2)
Q Exactive (2)
Q Exactive HF (2)
Liquid Chromatography MS - positive - reverse-phase (2)
Liquid Chromatography MS - negative - reverse phase (2)
Liquid Chromatography MS - positive - reverse phase (2)
10x chromium (1)
Lightwave (1)
Ultracentrifuge (1)
Spectronic Helios Alpha UV-Vis spectrophotometer (1)
Illumina Genome Analyzer II (1)
BGISEQ-500 (1)
Illumina NovaSeq 6000 (1)
- (1)
LTQ FT (1)
LTQ Orbitrap (1)
LTQ Orbitrap Velos (1)
Q Exactive HF-X (1)
Gas Chromatography MS - (1)
Direct infusion MS - negative (1)

Publication Date

2016 (71)
2014 (40)
2013 (22)
2012 (22)
2010 (22)
2015 (21)
2011 (20)
2025 (19)
2020 (18)
2022 (17)
2021 (17)
2017 (16)
2024 (15)
2019 (15)
2009 (15)
2008 (13)
2026 (10)
2018 (10)
2006 (10)
2023 (8)
2007 (8)
2005 (5)

CHEBI ID

CHEBI:219654 (1)
CHEBI:80074 (1)
CHEBI:6820 (1)
CHEBI:89974 (1)
CHEBI:89541 (1)
CHEBI:88875 (1)
CHEBI:88945 (1)
CHEBI:89953 (1)
CHEBI:90051 (1)
CHEBI:75846 (1)
CHEBI:89968 (1)
CHEBI:77163 (1)
CHEBI:89309 (1)
CHEBI:72840 (1)
CHEBI:84472 (1)
CHEBI:75385 (1)
CHEBI:88680 (1)
CHEBI:84848 (1)
CHEBI:86162 (1)
CHEBI:89372 (1)
CHEBI:185794 (1)
CHEBI:89842 (1)
CHEBI:4458 (1)
CHEBI:81175 (1)
CHEBI:133142 (1)
CHEBI:88430 (1)
CHEBI:74619 (1)
CHEBI:88443 (1)
CHEBI:75101 (1)
CHEBI:89092 (1)

Metabolite Name

Sterculic acid (2)
Heptadecanoic acid (2)
10-Deoxymethynolide (2)
Perindopril (2)
L-Erythrulose (2)
Maleic acid (2)
Allantoin (2)
Xylitol (2)
Succinic Acid (2)
Tetrocarcin A (1)
Akeboside Ste (1)
ÎÛ-CEHC (1)
(2S)-4-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl-(carboxylatomethyl)sulfonio]-2-azaniumylbutanoate (1)
(2S)-2-azaniumyl-3-(7-chloro-1H-indol-3-yl)propanoate (1)
2-hydroxy-1-[(3R,10S,11S,13S,17R)-3,11,17-trihydroxy-10,13-dimethyl-1,2,3,4,5,6,7,8,9,11,12,14,15,16-tetradecahydrocyclopenta[a]phenanthren-17-yl]ethanone (1)
[4,5,6-trihydroxy-2-(hydroxymethyl)oxan-3-yl] 2-(1H-indol-3-yl)acetate (1)
3-(1H-imidazol-5-ylmethyl)-6-(1H-indol-3-ylmethyl)piperazine-2,5-dione (1)
[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] benzoate (1)
2-amino-9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H-purin-6-one (1)
Val Glu Phe Asp (1)
Trioxilin B3;(5Z,8Z,14Z)-(11R,12R)-10,11,12-Trihydroxyeicosa-5,8,14-trienoic acid;(5Z,8Z,14Z)-(11R,12R)-10,11,12-Trihydroxyicosa-5,8,14-trienoic acid (1)
Toxicarol;alpha-Toxicarol (1)
Thr Lys Asn Glu (1)
Phe Asn Thr Lys (1)
N-hexadecyl hydroxyproline (1)
N-Acetyl-L-2-amino-6-oxopimelate;L-2-Acetamido-6-oxoheptanedioate;L-2-Acetamido-6-oxopimelate (1)
N-Acetyl-D-fucosamine;2-Acetamido-2,6-dideoxy-D-galactose (1)
Melibiitol;6-O-alpha-D-Galactosyl-D-glucitol (1)
Lys Ile Asn Glu (1)
Lys Asn Gln Glu (1)

First Public Date

2013 (226)
2024 (84)
2021 (70)
2015 (69)
2016 (68)
2014 (66)
2022 (63)
2026 (61)
2025 (59)
2020 (57)
2019 (50)
2023 (42)
2018 (32)
2017 (23)
2012 (6)
2011 (3)
2010 (2)

Modelling Approach

Constraint-based model (1)
Ordinary differential equation model (1)

Lab affiliation

Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria (4)
Pacific Northwest National Laboratory (3)
Proteomics (3)
Defence Research & Development Establishment, Gwalior. (2)
Bavarian Center for Biomolecular Mass Spectrometry Gregor-Mendel-Strasse 4 85354 Freising Germany (1)
CEA-Marcoule, ProGenoMIX platform, DRF-Li2D, 30207 Bagnols-sur-Ceze, France (1)
Chemical and Biological Signatures Group, Pacific Northwest National Laboratory (1)
Department Molekulare Systembiologie Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Permoserstraße 15 | 04318 Leipzig (1)
Department of Immunobiology, University of Lausanne, Switzerland (1)
ETH Zurich Institute of Molecular Biology & Biophysics (1)
Institut Pasteur, Universite Paris Cite, CNRS UMR6047, Yersinia Research Unit, Paris,France (1)
Institut für Medizinische Mikrobiologie und Hygiene Elfriede-Aulhorn-Str. 6 72076 Tübingen Germany (1)
Institut für Medizinische Mikrobiologie und Hygiene Universitätsklinikum Tübingen Elfriede-Aulhorn-Str. 6 72076 Tübingen Germany (1)
Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany (1)
Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz Parana, Parana, Brazil (1)
Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA. (1)
Max Planck Insitut for Terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany (1)
Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany (1)
Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch-Str. 10 35043 Marburg Germany (1)
Max von Pettenkofer-Institut (1)
Pacific Northwest National Laboratory, Richland WA USA (1)
Quadram Institute Bioscience, Norwich Research Park, NR4 7UA (1)
School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Queensland 4072, Australia ARC Industry Transformation Training Centre for Cryo-electron Microscopy of Membrane Proteins Institute for Molecular Bioscience, The University of Queensland, St Lucia Queensland 4072, Australia (1)
Umea University (1)
University of Florida (1)
Yersinia Research Unit Duclaux Building, Bertrand wing – Ground Floor Institut Pasteur, 28, rue du Docteur Roux 75015 Paris (1)

IsPrivate

False (2)

Submitter Keywords

FROG (1)

Classification

bacteria (666)
viruses (18)

Modification

Not available (3)

Study type

Transcription profiling by array (119)
RNA-seq of coding RNA (39)
ChIP-seq (5)
RNA-seq of non coding RNA (5)
ChIP-chip by array (4)
Comparative genomic hybridization by array (3)
Other (3)
High-throughput sequencing (2)
Animal - High-throughput sequencing (2)
Methylation profiling by high throughput sequencing (2)
Genotyping by mass spectrometer (1)
Unknown experiment type (1)
Cell line - High-throughput sequencing (1)
Transcription profiling by tiling array (1)
RNAi profiling by array (1)
Methylation profiling by array (1)
RNA-seq of total RNA (1)

Release Date

2021 (143)
2022 (137)
2016 (133)
2015 (129)
2014 (127)
2025 (123)
2023 (112)
2020 (110)
2019 (104)
2012 (102)
2017 (99)
2011 (97)
2018 (94)
2010 (91)
2013 (89)
2024 (84)
2009 (71)
2008 (55)
2006 (45)
2007 (33)
2005 (33)
2004 (28)
2002 (28)
1999 (28)
2000 (26)
2003 (24)
2001 (23)
1998 (21)
2026 (15)
1997 (2)

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Human Archaeological Dentin as Source of Polar and Less Polar Metabolites for Untargeted Metabolomic Research: The Case of Yersinia pestis

Metabolomic approaches, such as in clinical applications of living individuals, have shown potential use for solving questions regarding the past when applied to archaeological material. Here, we study for the first time the potential of this Omic approach as applied to metabolites extracted from ar...

2024-03-15 | MTBLS7394 | MetaboLights

The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [rovA mutant]

Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII. The Y. pseudotuberculosis rovA regulon was determined in Yersinia minimal minimum developed for the study. RovA is a key regulator for Yersinia virulence. Y. pseudotuberculosis YPIII or the isogenic rovA mutant strain w...

ORGANISM(S): Yersinia pseudotuberculosis

2014-09-17 | E-GEOD-54546 | biostudies-arrayexpress

The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [csrA mutant]

Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII. The Y. pseudotuberculosis csrA regulon was determined in Yersinia minimal minimum developed for the study. CsrA is a key regulator coordinating virulence and metabolism. Y. pseudotuberculosis YPIII or the isogenic csrA m...

ORGANISM(S): Yersinia pseudotuberculosis

2014-09-17 | E-GEOD-54545 | biostudies-arrayexpress

The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [crp mutant]

Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII. The Y. pseudotuberculosis crp regulon was determined in Yersinia minimal minimum developed for the study. Crp is a key regulator coordinating virulence and metabolism. Y. pseudotuberculosis YPIII or the isogenic crp muta...

ORGANISM(S): Yersinia pseudotuberculosis

2014-09-17 | E-GEOD-54544 | biostudies-arrayexpress

Phenotypic and transcriptional analysis of the osmotic regulator OmpR in Yersinia pestis

Background The osmotic regulator OmpR in Escherichia coli regulates differentially the expression of major porin proteins OmpF and OmpC. In Yersinia enterocolitica and Y. pseudotuberculosis, OmpR is required for both virulence and survival within macrophages. However, the phenotypic and regulatory r...

ORGANISM(S): Yersinia pestis

2011-10-23 | E-GEOD-26601 | biostudies-arrayexpress

Transcriptional analysis of quorum sensing deficient in Yersinia pestis CO92 at 37M-BM-0C

Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of quorum sensing was investigated by comparing transcript profiles when three quorum-sensing synthase genes are knocked out....

ORGANISM(S): Yersinia pestis

2013-09-05 | E-GEOD-21911 | biostudies-arrayexpress

Transcriptional analysis of luxS-null strain in Yersinia pestis CO92 at 37M-BM-0C

Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of autoinducer 2 (AI-2) quorum sensing was investigated by comparing transcript profiles when luxS gene was knocked out. The ...

ORGANISM(S): Yersinia pestis

2013-09-05 | E-GEOD-22849 | biostudies-arrayexpress

Transcription profiling of Yersinia pestis dam mutant that has attenuated virulence in mice

We have constructed a dam mutant of Yersinia pestis GB. In BALB/c mice inoculated subcutaneously, the median lethal dose of the mutant was at least 2000-fold higher than the wild type. Mice inoculated with sub-lethal doses of the mutant were protected against a subsequent challenge with virulent Y. ...

ORGANISM(S): Yersinia pestis

2007-01-30 | E-BUGS-32 | biostudies-arrayexpress

In-host evolution of Yersinia enterocolitica during a chronic human infection

Following a pacemaker implantation, a 75-years-old patient suffered from five successive bacteremia episodes between in 1999 and 2013, during which five bacterial strains were isolated. Phenotypic and whole-genome sequencing analysis of four isolates identified the strains as Yersinia enterocolitica...

ORGANISM(S): Yersinia enterocolitica Bacteria

2025-05-26 | PXD043567 | Pride

Transcription analysis of AI-2 signal add in experiment in Yersinia pestis CO92 at 37M-BM-0C

Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of autoinducer-2 (AI-2) quorum sensing was investigated by comparing transcript profiles when AI-2 quorum-sensing signal is a...

ORGANISM(S): Yersinia pestis

2013-09-05 | E-GEOD-22848 | biostudies-arrayexpress

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