Pseudomonas putida kt2440

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Unknown (349)
Genomics (342)
Transcriptomics (127)
Proteomics (69)
Models (8)
Metabolomics (3)
Other (1)

Organisms

Pseudomonas putida KT2440 (92)
Pseudomonas putida (59)
Pseudomonas (11)
Escherichia coli (10)
Corynebacterium glutamicum (8)
Bacillus subtilis subsp. subtilis str. 168 (7)
Pseudomonas aeruginosa (5)
Gluconobacter oxydans (5)
Escherichia coli K-12 (5)
Pseudomonas aeruginosa PAO1 (5)
Plasmid RP4 (4)
Pseudomonas fluorescens Pf0-1 (3)
Metapseudomonas resinovorans (2)
Allochromatium vinosum DSM 180 (2)
Corynebacterium glutamicum ATCC 13032 (2)
Gluconobacter oxydans 621H (2)
Pseudomonas fluorescens (2)
Escherichia coli str. K-12 substr. MG1655 (2)
Microbacterium oxydans (1)
Solanum lycopersicum (1)
Pseudomonas chlororaphis subsp. chlororaphis (1)
Pseudomonas putida DOT-T1E (1)
Pseudomonas protegens (1)
Pseudomonas chlororaphis (1)
Pseudideonella sakaiensis (1)
Acinetobacter baylyi (1)
Pseudomonas protegens CHA0 (1)
Rhodobacter capsulatus SB 1003 (1)
Bacillus subtilis (1)
Escherichia coli BW25113 (1)

Organisms

Pseudomonas putida KT2440 (183)
Pseudomonas putida (63)
fungus metagenome (30)
prokaryotic metagenome (9)
Pseudomonas aeruginosa (1)
Pseudideonella sakaiensis (1)
rhizosphere metagenome (1)

Repository

ENA (339)
geo (87)
pride (50)
biostudies-arrayexpress (43)
MassIVE (12)
BioModels (5)
PanoramaPublic (5)
Cell Collective (3)
iProX (2)
MetaboLights (2)
EVA (1)
GNPS (1)

Tissue

Cell culture (8)
Cell lysate (4)
Cell line cell (2)
Endothelial tube (1)
Endospore (1)
Cell suspension culture (1)

Technology Type

Mass Spectrometry (50)
Shotgun proteomics (22)
Bottom-up proteomics (20)
Data-independent acquisition (17)
Affinity purification coupled with mass spectrometry proteomics (5)
Data-dependent acquisition (4)
SWATH MS (4)
Mass spectrometry (2)
Top-down proteomics (2)
Metaproteomics (1)
Gel-based experiment (1)

Instrument Platform

Q Exactive Plus (4)
LTQ Orbitrap Elite (3)
Q Exactive (2)
Orbitrap Eclipse (2)
Liquid Chromatography MS - negative - reverse phase (2)
ScanArray 4000 [PerkinElmer] (1)
ScanArray Lite [PerkinElmer] (1)
GenePix Personal 4100A [Axon Instruments] (1)
Illumina NovaSeq 6000 (1)
Illumina HiSeq 2000 (1)
NextSeq 500 (1)
- (1)
Agilent 8890 GC-MS (1)
LTQ Orbitrap Velos (1)
Orbitrap Exploris 480 (1)
Q Exactive HF-X (1)

Publication Date

2025 (23)
2011 (18)
2023 (16)
2013 (14)
2026 (13)
2015 (12)
2022 (12)
2020 (12)
2024 (11)
2021 (11)
2012 (10)
2010 (10)
2018 (10)
2019 (9)
2014 (8)
2017 (7)
2016 (3)
2007 (3)
2009 (2)
2008 (2)
2006 (1)

CHEBI ID

CHEBI:62959 (1)
CHEBI:62958 (1)
CHEBI:32797 (1)
CHEBI:380 (1)
CHEBI:11036 (1)
CHEBI:16782 (1)
CHEBI:18739 (1)
CHEBI:18738 (1)
CHEBI:62621 (1)
CHEBI:26638 (1)
CHEBI:47569 (1)
CHEBI:9098 (1)
CHEBI:27277 (1)
CHEBI:30816 (1)
CHEBI:46315 (1)
CHEBI:27278 (1)
CHEBI:15301 (1)
CHEBI:9933 (1)
CHEBI:16632 (1)
CHEBI:46497 (1)
CHEBI:46502 (1)
CHEBI:36272 (1)
CHEBI:30518 (1)
CHEBI:36271 (1)
CHEBI:26894 (1)
CHEBI:9474 (1)
CHEBI:45729 (1)
CHEBI:27902 (1)
CHEBI:71392 (1)
CHEBI:77932 (1)

Metabolite Name

3-phosphoglyceric acid (1)
Gluconate (1)
Fumarate (1)
6-phosphogluconic acid (1)
Aspartic acid (1)
Alpha-ketoglutaric acid (1)
Dihydroxyacetone phosphate (1)
Phosphoenolpyruvate (1)
Succinate (1)
Glucose 6-phosphate (1)
Fructose 6-phosphate (1)
Pyruvate (1)
Malate (1)
Citrate (1)

IsPrivate

False (5)

Model Flag

Non Kinetic (4)

Submitter Keywords

FROG (1)

First Public Date

2019 (87)
2024 (70)
2018 (38)
2025 (28)
2014 (25)
2017 (23)
2026 (20)
2020 (18)
2022 (12)
2021 (5)
2015 (4)
2013 (4)
2023 (3)
2016 (2)

Classification

bacteria (1)

Modelling Approach

Constraint-based model (4)

Study type

Transcription profiling by array (26)
RNA-seq of coding RNA (8)
Transcription profiling by tiling array (7)
ChIP-chip by tiling array (1)
ChIP-chip by array (1)

Release Date

2020 (39)
2024 (31)
2021 (31)
2025 (30)
2022 (26)
2023 (23)
2019 (22)
2017 (21)
2014 (20)
2016 (19)
2018 (19)
2012 (17)
2011 (14)
2013 (13)
2010 (13)
2015 (12)
2009 (10)
2007 (8)
2008 (6)
2006 (5)
2000 (5)
2026 (2)
2004 (2)
2002 (2)
2005 (1)
1998 (1)

Lab affiliation

Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720 (22)
CEA, DRF, IBiTec-S, SPI, Li2D, Laboratory "Innovative technologies for Detection and Diagnostics" (3)
Biotechnology Research Center, The University of Tokyo, Tokyo, Japan. (2)
Helmholtz Centre for Environmental Research - UFZ, Environmental Biotechnology and Technische Universität Berlin, Geobiotechnology (2)
Biotechnology Research Center, The University of Tokyo (1)
Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia, 4072 (1)
University of Tartu, Institute of Molecular and Cell Biology, Department of Genetics (1)
Estonia University of Tartu Faculty of Science and Technology Institute of Molecular and Cell Biology Chair of Genetics (1)
Biotechnology Research Center, The University of Tokyo. (1)
Department of Bioprocess Engineering (150k), Institute of Food Science and Biotechnology (150), University of Hohenheim, Fruwirthstr. 12, 70599 Stuttgart, Germany (1)
University of Hohenheim, Prof. Rudolf Hausmann (1)
University of Stuttgart, Institute of Biochemistry and Technical Biochemistry, Department of Technical Biochemistry,Stuttgart, Germany (1)
UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland BEACON - Bioeconomy Research centre, Ireland, University College Dublin, Belfield, Dublin 4, Ireland (1)
UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland BiOrbic - Bioeconomy Research centre, Ireland, University College Dublin, Belfield, Dublin 4, Ireland (1)
School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland (1)
Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia (1)
Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich (TUM), Ernst-Otto-Fischer-Stra?e 8, 85748 Garching, Germany (1)
Lawrence Berkeley National Laboratory (1)
Advanced Water Management Centre, The University of Queensland (1)
Polymer Biotechnology Lab Centro de Investigaciones Biologicas(CIB) Consejo Superior de Investigaciones Científicas (CSIC) C/ Ramiro de Maeztu, 9. 28040 Madrid, Spain (1)
CEA-Marcoule, ProGenoMIX platform, DRF-Li2D, 30207 Bagnols-sur-Ceze, France (1)
Pacific Northwest National Laboratory, USA (1)
Pacific Northwest National Laboratory (1)
USDA-ARS (1)
Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic (1)

Tags

pathogen (1)
pathogen:bacterium (1)

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Glyceraldehyde-3-phosphate dehydrogenase homologs as bifunctional gatekeepers of metabolic segregation in Pseudomonas putida

Metabolically versatile Pseudomonas species can assimilate various glycolytic and gluconeogenic substrates. Simultaneous assimilation is known to involve segregating carbons from each substrate type into different metabolic pathways, but the mechanisms that govern this segregation remain unresolv...

2025-11-03 | MTBLS12468 | MetaboLights

3CB-induced gene expression of Pseudomonas putida KT2440/pSL1 in soil (with RNA amplification)

Genome-wide scanning of gene expression by microarray techniques was successfully performed on RNA extracted from a sterilized soil inoculated with Pseudomonas putida KT2440/pSL1, which contains a chloroaromatic degrading plasmid, in the presence or absence of 3-chlorobenzoic acid (3CB). The genes s...

ORGANISM(S): Pseudomonas putida KT2440

2011-03-29 | E-GEOD-28215 | biostudies-arrayexpress

KT2440 vs KT2440_NAH7

Plasmid-free Pseudomonas putida KT2440 compared with the same strain harbouring NAH7 plasmid; all the cells were grown in minimal medium M9 with glucose

ORGANISM(S): Pseudomonas putida

2012-07-27 | E-MEXP-3412 | biostudies-arrayexpress

KT2440 vs. KT2440 _NAH7 Naphthalene

Plasmid-free Pseudomonas putida KT2440 compared with the same strain harbouring NAH7 plasmid; all the cells were grown in minimal medium (M9 with glucose) saturated with naphthalene.

ORGANISM(S): Pseudomonas putida

2012-07-27 | E-MEXP-3411 | biostudies-arrayexpress

Expression data from Pseudomonas putida KT2440

In this study we exploited next-generation Illumina sequencing technology (Wang et al., 2009) to refine the current annotation of the KT2440 genome. Transcriptome sequencing data were queried for yet undescribed small RNAs and ORFs and employed to validate predicted operons and gene coordinates. Exp...

ORGANISM(S): Pseudomonas putida KT2440

2011-03-25 | E-GEOD-24176 | biostudies-arrayexpress

Pseudomonas putida KT2440 cells: control vs. 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA)

Transcriptome profiling of Pseudomonas putida KT2440 comparing cells exposed for 1 hour to DIMBOA from maize (Zea mays) to unexposed cells Two-condition experiment, unexposed vs. exposed, three biological replicates independantly grown and harvested. A dye swap was performed on each biological repli...

ORGANISM(S): Pseudomonas putida KT2440

2012-07-08 | E-GEOD-36489 | biostudies-arrayexpress

Expression data from Pseudomonas putida KT2440 (RNA-Seq data)

We used cDNA generated from total mRNA for RNA-Seq analysis (Genome Analyzer II at GATC Biotech AG) to monitore the gene expression of P. putida after a cold shock from 30M-BM-0C to 10M-BM-0C Culture was grown in minimal medium supplemented with succinate at 30M-BM-0C. In mid-exp. phase cells were ...

ORGANISM(S): Pseudomonas putida KT2440

2011-02-01 | E-GEOD-24175 | biostudies-arrayexpress

Transcription profiling by array of Pseudomonas putida KT2440 during exponential phase growing in minimal medium with or without naphthalene

Transcriptional profile of Pseudomonas putida KT2440 during exponential phase growing in minimal medium saturated with naphthalene compared with the same strain in naphthalene-free medium.

ORGANISM(S): Pseudomonas putida

2010-11-01 | E-MEXP-2823 | biostudies-arrayexpress

Transcription profiling of P. putida KT2440 cultivated at 7 bar and at 7 bar with elevated dissolved oxygen tension

We investigated the changes of gene expression in PHA-producing Pseudomonas putida KT2440 cultivated under elevated pressure (7 bar) and under combined elevated pressure (7 bar) and elevated dissolved oxygen tension by means of DNA microarrays. RNA samples were isolated from cells cultivated in chem...

ORGANISM(S): Pseudomonas putida

2012-12-03 | E-MEXP-3632 | biostudies-arrayexpress

Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440

Lignin modifications and the exoproteome of three aromatic catabolic bacteria: Pseudomonas putida KT2440, Rhodoccocus jostii RHA1, and Amycolatopsis sp. ATCC 39116. Samples were digested with trypsin, then analyzed by LC-MS/MS. Data was searched with MSGF+ and abundances inferred using PNNL's DMS an...

ORGANISM(S): Pseudomonas Putida Kt2440 (ncbitaxon:160488) Amycolatopsis Sp. Atcc 39116 (ncbitaxon:385957) Rhodococcus Jostii Rha1 (ncbitaxon:101510)

2019-11-01 | MSV000084524 | MassIVE

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