Bacteria viability

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Unknown (2097)
Genomics (222)
Transcriptomics (150)
Proteomics (39)
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Models (2)
Other (2)
Methylation profiling (1)

Organisms

Homo sapiens (22)
Escherichia coli (16)
Burkholderia cenocepacia (7)
Bacillus subtilis (7)
Mus musculus (6)
Bacillus subtilis subsp. subtilis str. 168 (5)
Caulobacter vibrioides (5)
Staphylococcus aureus (5)
Caenorhabditis elegans (4)
Escherichia coli str. K-12 substr. MG1655 (4)
Candida albicans (4)
Streptococcus pneumoniae R6 (4)
Pseudomonas aeruginosa (4)
Rhodospirillum rubrum (3)
Pseudomonas aeruginosa PAO1 (3)
Myxococcus xanthus (2)
Campylobacter jejuni subsp. jejuni 81-176 (2)
Geobacter metallireducens (2)
Francisella tularensis subsp. tularensis SCHU S4 (2)
Streptococcus mutans (2)
Coxiella burnetii (2)
Haemophilus influenzae 22.1-21 (1)
Magnetospirillum gryphiswaldense (1)
Bacillus subtilis subsp. subtilis str. JH642 (1)
Methanobrevibacter ruminantium (1)
Bifidobacterium animalis subsp. lactis Bl-04 (1)
Fusarium oxysporum (1)
Sphingomonas sp. LH128 (1)
Lactococcus lactis (1)
Bifidobacterium breve UCC2003 (1)

Organisms

Escherichia coli (15)
Homo sapiens (10)
Pseudomonas aeruginosa (7)
Staphylococcus aureus (5)
Escherichia coli K-12 (4)
Mycobacterium tuberculosis (4)
Escherichia coli str. K-12 substr. MG1655 (3)
Streptococcus pneumoniae R6 (2)
Caulobacter vibrioides CB15 (2)
Escherichia coli ATCC 8739 (2)
Lactococcus lactis subsp. lactis Dephy 1 (2)
Campylobacter jejuni subsp. jejuni 81-176 (2)
Caulobacter vibrioides (2)
Escherichia coli BW25113 (2)
Campylobacter jejuni (2)
Streptococcus pneumoniae (2)
Bacteria (2)
Acinetobacter baumannii (2)
Pseudomonas aeruginosa PAO1 (2)
Campylobacter jejuni subsp. jejuni 81116 (1)
Wigglesworthia glossinidia (1)
Borreliella burgdorferi B31 (1)
Bacillus subtilis subsp. subtilis str. SMY (1)
Francisella tularensis subsp. tularensis SCHU S4 (1)
Paramagnetospirillum magneticum AMB-1 (1)
Mesorhizobium robiniae (1)
Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (1)
Escherichia coli str. K-12 substr. MC4100 (1)
Escherichia coli W (1)
Corynebacterium glutamicum ATCC 13032 (1)

Repository

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biostudies-arrayexpress (106)
geo (54)
pride (28)
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Tissue

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CACO-2 cell (1)
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Enterocyte (1)
Extracellular vesicle (1)
Fibroblast (1)
HeLa cell (1)

Disease

Hemolytic-uremic syndrome (1)
Primary tuberculosis (1)

Technology Type

Mass Spectrometry (28)
Shotgun proteomics (11)
Bottom-up proteomics (9)
Mass spectrometry (4)
Data-independent acquisition (4)
Affinity purification coupled with mass spectrometry proteomics (3)
Data-dependent acquisition (3)
Gel-based experiment (3)
HDMSE (2)
MSE (2)
Mass spectrometry assay (1)
Proteogenomics (1)
SWATH MS (1)

Instrument Platform

Illumina NovaSeq 6000 (3)
Illumina HiSeq 2000 (2)
Liquid Chromatography MS - negative - hilic (2)
Liquid Chromatography MS - positive - hilic (2)
Thermal cycler; magnetic separation rack; Qubit Fluorometer; Agilent TapeStation 4200 (1)
Microcentrifuge; magnetic separation rack; Qubit Flu/spectrophotometer; Agilent TapeStation 4200 (1)
Incubator shaker; spectrophotometer; Cmag measurement system; flow cytometer (1)
Element AVITI (1)
Geniom RT Analyzer (1)
Geniom (1)
GenePix 4200AL (1)
BAS-1800 [FUJIFILM] (1)
Illumina MiSeq (1)
Illumina HiSeq 2500 (1)
NextSeq 500 (1)
LTQ Orbitrap XL (1)
Orbitrap Eclipse (1)
Orbitrap Exploris 480 (1)
Orbitrap Fusion Lumos (1)
Q Exactive HF-X (1)
Liquid Chromatography MS - (1)
Exactive (Thermo Scientific) (1)
Liquid Chromatography MS - negative - reverse phase (1)

Publication Date

2012 (25)
2015 (19)
2026 (18)
2010 (18)
2023 (15)
2024 (15)
2016 (15)
2008 (15)
2022 (9)
2021 (9)
2013 (8)
2025 (8)
2011 (7)
2020 (6)
2014 (5)
2018 (3)
2005 (2)
2017 (2)
2009 (2)
2007 (2)
2019 (1)
2006 (1)

UNIPROT ID/AC

P44461 (1)
P44460 (1)
P44462 (1)
P44458 (1)
P44459 (1)
Q57306 (1)
P44656 (1)
P44658 (1)
P44526 (1)
P44692 (1)
P44691 (1)
P44137 (1)
P44136 (1)
P44401 (1)
P44398 (1)
P45046 (1)
P45045 (1)
P45047 (1)
P44990 (1)
P43834 (1)
P44046 (1)
P44392 (1)
P44391 (1)
P44393 (1)
P45117 (1)
P43857 (1)
P44722 (1)
P43890 (1)
P43920 (1)
P43948 (1)

CHEBI ID

CHEBI:6328 (1)
CHEBI:21427 (1)
CHEBI:13191 (1)
CHEBI:9733 (1)
CHEBI:27126 (1)
CHEBI:15262 (1)
CHEBI:15263 (1)
CHEBI:9732 (1)
CHEBI:27125 (1)
CHEBI:15261 (1)
CHEBI:27127 (1)
CHEBI:27392 (1)
CHEBI:71573 (1)
CHEBI:58510 (1)
CHEBI:9807 (1)
CHEBI:22095 (1)
CHEBI:61494 (1)
CHEBI:8171 (1)
CHEBI:45209 (1)
CHEBI:21991 (1)
CHEBI:45080 (1)
CHEBI:45158 (1)
CHEBI:37788 (1)
CHEBI:45187 (1)
CHEBI:61528 (1)
CHEBI:61502 (1)
CHEBI:71316 (1)
CHEBI:58208 (1)
CHEBI:21295 (1)
CHEBI:6219 (1)

Metabolite Name

Nicotinamide (2)
Adenosine (2)
Guanosine (2)
CMP-Leg (1)
Leg (1)
5'-Adenylic acid, pentakis(trimethylsilyl) deriv. (1)
3-Methoxy-N,N,O-tris(trimethylsilyl)tyramine (1)
Metoprolol di-TMS derivative (1)
Propanolol TMS derivative (1)
Ricinoleic acid, trimethylsiloxy, trimethylsilyl ester (1)
N,O-Bis-(trimethylsilyl)-2-pyrrolidone carboxylic acid (1)
2-Piperidinecarboxylic acid, 1-(trimethylsilyl)-, trimethylsilyl ester (1)
Eicosane, 2-methyl- (1)
D-Glucuronic acid, 2,3,4,5-tetrakis-O-(trimethylsilyl)-, trimethylsilyl ester (1)
4-Propoxy-2-butanone (1)
L-Leucine, N-(trimethylsilyl)-, trimethylsilyl ester (1)
Alpha-D-Mannopyranose, 1,2,3,4,6-pentakis-O-(trimethylsilyl)- (1)
L-Valine, N-(trimethylsilyl)-, trimethylsilyl ester (1)
1-Cyclohexene-1-carboxylic acid, 3,4,5-tris[(trimethylsilyl)oxy]-, trimethylsilyl ester, [3R-(3 alpha,4 alpha,5 beta)]- (1)
L-Norleucine, N-(trimethylsilyl)-, trimethylsilyl ester (1)
Alpha-Naphthyl myristate (1)
Silanamine, N-[2-[3,4-bis[(trimethylsilyl)oxy]phenyl]ethyl]-1,1,1-trimethyl-N-(trimethylsilyl)- (1)
Sulfurous acid, dipropyl ester (1)
Phosphoric acid, 2-(trimethylsiloxy)-1-[(trimethylsiloxy)methyl]ethyl bis(trimethylsilyl) ester (1)
L-Aspartic acid, N-(trimethylsilyl)-, bis(trimethylsilyl) ester (1)
Heptadecane, 2,6-dimethyl- (1)
Butanoic acid, 2,4-bis[(trimethylsilyl)oxy]-, trimethylsilyl ester (1)
Succinic acid d4 (1)
1-Octanamine, n-octyl- (1)
Glycine d5 (1)

First Public Date

2026 (34)
2025 (28)
2024 (28)
2014 (28)
2023 (16)
2022 (13)
2020 (13)
2021 (12)
2017 (10)
2016 (8)
2018 (7)
2015 (6)
2013 (6)
2019 (5)
2012 (1)

Modelling Approach

Constraint-based model (1)

Lab affiliation

Anses Fougères (1)
Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany (1)
Biological Mass Spectrometry Lab,Department of Translational Medicine (DiMeT),Center for Translational Research on Autoimmune & Allergic Diseases - CAAD,University of Piemonte Orientale, Corso Trieste 15/A, 28100, Novara, Italy (1)
Chair of Organic Chemistry II, Technical University of Munich (1)
Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, District: Nadia, West Bengal, Pin Code: 741246, India (1)
Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Germany (1)
Department of Civil and Environmental Engineering, National University of Singapore (1)
Department of Clinical and Molecular Medicine Faculty of Medicine and Health Sciences Norwegian University of Science and Technology Trondheim, Norway (1)
Department of Metabolic Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, The Netherlands (1)
Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd. E., Guelph, Ontario, Canada, N1G 2W1 (1)
IPBS-Toulouse BP64182 205 route de Narbonne 31077 Toulouse Cedex04 (1)
Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, 31077, France (1)
LIST-ERIN-BEAP, Bascharage, Luxembourg (1)
Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET) (1)
Laboratory of Technology and Development: Meat and Meat Products (Tecno I), Reference Center for Lactobacilli (CERELA CONICET-FML-FCIC), Batalla de Chacabuco 145, 4000 San Miguel de Tucumán, Tucumán, Argentina (1)
Laboratório de Biotecnologia (Unidade de Biologia Integrativa, Setor de Genômica e Proteômica), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, Brazil (1)
Molecular and Cellular Biology, University of Guelph, Canada (1)
NICM HRI, Western Sydney University, NSW, Australia (1)
Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Kemitorvet, DK-2800 Lyngby, Denmark (1)
OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands (1)
Philipps-University Marburg, Department of Chemistry & SYNMIKRO, Hans-Meerwein-Straße, 35043 Marburg, GERMANY (1)
Proteomics and Metabolomics Facility, University of Nebraska- Lincoln (1)
Research Group of Microbiology, Vrije Universiteit Brussel, Brussels, Belgium (1)
Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany (1)
Ruhr-Universität Bochum Applied Microbiology Universitätsstr. 150 44780 Bochum Germany (1)
The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel (1)
de Duve Institute, Université catholique de Louvain (UCLouvain), Avenue Hippocrate 75, 1200 Brussels, Belgium (1)
i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Ipatimup – Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; (1)

IsPrivate

False (2)

Model Flag

Non Kinetic (1)

Submitter Keywords

FROG (1)

Classification

bacteria (78)
viruses (1)
protozoa (1)

Study type

Transcription profiling by array (74)
RNA-seq of coding RNA (14)
Unknown experiment type (4)
Transcription profiling by tiling array (3)
RNA-seq of non coding RNA (2)
ChIP-chip by tiling array (1)
High-throughput sequencing (1)
RNAi profiling by array (1)
RIP-seq (1)
Other (1)
ChIP-seq (1)
DNA-seq (1)
RNA-seq of coding RNA from single cells (1)
Methylation profiling by high throughput sequencing (1)

Release Date

2025 (240)
2023 (228)
2022 (225)
2024 (211)
2021 (196)
2020 (162)
2019 (134)
2018 (115)
2016 (115)
2015 (106)
2017 (97)
2012 (56)
2010 (46)
2014 (44)
2013 (41)
2026 (38)
2011 (34)
2008 (32)
2009 (16)
2006 (15)
2007 (14)
2004 (9)
2005 (8)
2003 (6)
2001 (6)
2002 (5)
2000 (2)
1998 (2)

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Sensing prokaryotic mRNA signifies microbial viability and promotes immunity

MyD88-independent signal transduction associated with Toll-like receptors (TLRs) 3 and TLR4 is mediated through the adapter protein TRIF (TIR-domain-containing adapter-inducing interferon-beta). It has been proposed that TLR signalling is important for the transcription of crucial inflammasome compo...

ORGANISM(S): Mus musculus

2011-05-22 | E-GEOD-27960 | biostudies-arrayexpress

The Methylomes of Six Bacteria

Six bacterial genomes, Geobacter metallireducens GS-15, Chromohalobacter salexigens, Vibrio breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni subsp. jejuni 81-176 and Campylobacter jejuni NCTC 11168, all of which had previously been sequenced using other platforms were re-sequenced u...

ORGANISM(S): Geobacter metallireducens

2012-10-04 | E-GEOD-40133 | biostudies-arrayexpress

Suppressor mutant screening lacking growth-essential tRNA modification in bacteria

Post-transcriptional modifications are important for transfer RNAs (tRNAs) to be efficient and accurate in translation on the ribosome. The m1G37 modification on a subset of tRNAs in bacteria are generated by a conserved methyltransferase TrmD and is essential for bacterial growth. Previous studies ...

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

2022-09-24 | E-MTAB-12178 | biostudies-arrayexpress

Expression data from the commensal bacteria Escherchia coli strain HB101 interacting with Caenorhabditis elegans and/or Giardia duodenalis

Homeostatic interactions between the host and its resident microbiota is important for normal physiological functions and if altered, it could lead to dysbiosis, a change in the structure and function of the microbiota, and as a result to various pathophysiologies. Altered structure in bacterial com...

ORGANISM(S): Escherichia coli

2015-04-02 | E-GEOD-61092 | biostudies-arrayexpress

Developmental transitions of Coxiella burnetii grown in axenic media

Coxiella burnetii undergoes a biphasic developmental cycle within its host cell that generates morphologically and physiologically distinct large cell variants (LCV) and small cell variants (SCV). During the lag phase of the C. burnetii growth cycle, non-replicating SCV differentiate into replicati...

ORGANISM(S): Coxiella burnetii

2013-12-02 | E-GEOD-51135 | biostudies-arrayexpress

Metabolomics analysis reveals the participation of efflux pumps and ornithine in the response of Pseudomonas putida DOT-T1E cells to challenge with propranolol

Efflux pumps are critically important membrane components that play a crucial role in strain tolerance in Pseudomonas putida to antibiotics and aromatic hydrocarbons that result in these toxicants being expelled from the bacteria. Here, the effect of propranolol on P. putida was examined by sudden a...

2016-08-23 | MTBLS320 | MetaboLights

Transcriptional activity of Bacillus subtilis exposed to lethal heat stress

Transcriptional profiling of Bacillus subtilis to lethal heat stress by systematic sampling of bacterial cell suspensions exposed to gradually increasing temperatures. Keywords: Stress response Bacterial cell suspensions exposed to increasing temperatures ranging from 30-62ºC (Cy5 channel) versus 3...

ORGANISM(S): Bacillus subtilis

2008-12-07 | E-GEOD-12372 | biostudies-arrayexpress

An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene [array]

We studied the response to increased DNA-supercoiling in Streptococcus pneumoniae by using seconeolitsine (SCN), a DNA topoisomerase I inhibitor. A homeostatic transcriptional response allowing recovering of supercoiling density was observed in cells treated with subinhibitory SCN concentrations. Su...

ORGANISM(S): Streptococcus pneumoniae R6

2016-07-07 | E-GEOD-77587 | biostudies-arrayexpress

An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene [RNA-Seq]

ORGANISM(S): Streptococcus pneumoniae R6

2016-07-07 | E-GEOD-77748 | biostudies-arrayexpress

Metabolic recycling of engulfed bacteria in macrophages

Sensing of microbial viability orchestrates the metabolic recycling of engulfed bacteria in macrophages

PRJEB68361 | ENA

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