Iron depleted - OmicsDI

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2003 (1)
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UNIPROT ID/AC

ACCA_BORPE (1)
ACP_BORPE (1)
ALCA_BORPE (1)
AMPA_BORPE (1)
APAH_BORPE (1)
APT_BORPE (1)
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BVGA_BORPE (1)
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CH10_BORPE (1)

CHEBI ID

CHEBI:30769 (2)
CHEBI:6650 (2)
CHEBI:15356 (1)
CHEBI:15361 (1)
CHEBI:15595 (1)
CHEBI:15891 (1)
CHEBI:16027 (1)
CHEBI:16450 (1)
CHEBI:16668 (1)
CHEBI:16680 (1)
CHEBI:16810 (1)
CHEBI:16811 (1)
CHEBI:16856 (1)
CHEBI:17126 (1)
CHEBI:17822 (1)
CHEBI:17858 (1)
CHEBI:18237 (1)
CHEBI:21557 (1)
CHEBI:24898 (1)
CHEBI:24996 (1)
CHEBI:27570 (1)
CHEBI:28044 (1)
CHEBI:28300 (1)
CHEBI:28683 (1)
CHEBI:29016 (1)
CHEBI:29806 (1)
CHEBI:30031 (1)
CHEBI:37154 (1)
CHEBI:38263 (1)
CHEBI:53210 (1)

Metabolite Name

(+)-1,2-Dehydrotelobine (1)
(+)-2,7-Dideoxypancratistatin (1)
(+)-2-Amino-7-phosphonoheptanoic acid (1)
(+)-Cocsuline (1)
(+)-Codonopsine (1)
(+)-Epipinoresinol (1)
(+)-Erysotrine (1)
(+)-Neomenthyl O-beta-D-glucoside (1)
(+)-Neomethynolide (1)
(+)-Rauflexine (1)
(+)-cyclopentanecarboxylic acid (1)
(+/-)-Isobutyl 3-methylthiobutyrate (1)
(-)-(E)-Guggulsterone (1)
(-)-11-hydroxy-9,10-dihydrojasmonic acid 11-beta-D-glucoside (1)
(-)-11-nor-9-carboxy-Delta9-THC (1)
(-)-12-hydroxy-9,10-dihydrojasmonic acid (1)
(-)-20-Acetoy-9-hydroxy-1,6,14-rhamnofolane-triene-3,13-dione (1)
(-)-3,4-dimethoxy-3,4-desmethylenedioxycubebin (1)
(-)-Chicanine (1)
(-)-Hydroxycitric acid (1)
(-)-Isocelorbicol (1)
(-)-Mycestericin E (1)
(-)-Platyphyllide (1)
(-)-Sphingofungin E (1)
(-)-Syringolide 1 (1)
(-)-Tetrodecamycin (1)
(12S,15S)-15-O-Demethyl-10,29-dideoxy-11,12-dihydro-striatin C (1)
(1E,4E)-1,5-bis(4-methoxyphenyl)penta-1,4-dien-3-one (1)
(1R,10aS)-1,4,10,10a-tetrahydrophenazine-1,6-dicarboxylic acid (1)
(1R,5aS,6R)-1,4,5,5a,6,9-hexahydrophenazine-1,6-dicarboxylic acid (1)

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2014 (18)
2026 (10)
2020 (9)
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2023 (5)
2022 (5)
2015 (5)
2025 (4)
2019 (4)
2021 (3)
2017 (2)
2018 (1)
2016 (1)

Classification

bacteria (18)
fungi (8)
protozoa (1)

Study type

Transcription profiling by array (106)
RNA-seq of coding RNA (89)
Unknown experiment type (3)
ChIP-seq (3)
Methylation profiling by high throughput sequencing (3)
RNA-seq of non coding RNA (3)
High-throughput sequencing (2)
Transcription profiling by tiling array (2)
ChIP-chip by array (2)
Other (2)
DNA-seq (2)
Transcription profiling by SAGE (1)
Cell line - High-throughput sequencing (1)
Ribo-seq (1)
Methylation profiling by array (1)
Genotyping by high throughput sequencing (1)
RNA-seq of coding RNA from single cells (1)

Release Date

2015 (55)
2013 (48)
2022 (42)
2016 (41)
2023 (38)
2021 (38)
2025 (37)
2014 (35)
2024 (35)
2018 (34)
2020 (33)
2011 (33)
2010 (32)
2017 (27)
2012 (27)
2019 (22)
2008 (12)
2007 (11)
2009 (8)
2003 (6)
2026 (5)
2004 (4)
2006 (4)
2005 (3)
2000 (2)
1999 (2)
2002 (1)
2001 (1)

Lab affiliation

The Rockefeller University (2)
1.Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, 2.Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA, 3.Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. (1)
Boston College, Department of Chemistry (1)
Center for Integrative Infectious Diseases (CIID) Integrative Virology Heidelberg University Clinic Im Neuenheimer Feld 344 69120 Heidelberg (1)
Chemistry Department, Boston College, USA (1)
Departamento de Bioquímica y Biología Molecular. Edificio Severo Ochoa. Campus de Rabanales. Universidad de Córdoba. Córdoba, 14071. Spain (1)
Department of Biological Sciences University of Alberta G-504 Biological Sciences Bldg. Edmonton Alberta T6G 2E9 Canada (1)
Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA (1)
Department of Functional Genomics, Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany (1)
Department of Medical Microbiology and Parasitology, Universiti Putra Malaysia, Serdang 43400, Malaysia. (1)
Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand (1)
Department of Pathology and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA. (1)
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD USA (1)
Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany (1)
Glasgow Centre for Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK (1)
Head of the Mass Spec Devision at VetCore, Univeristy of Veterinary Medicine Vienna (1)
LPHI, Univ Montpellier, CNRS, INSERM, Montpellier, France (1)
Mass spectrometry research center, School of pharmacy University of Maryland, Baltimore (1)
Medizinisches Proteom-Center, Ruhr-Universität Bochum, ZKF 1.055, Universitätsstraße 150, 44801 Bochum, Germany (1)
Molecular and Cellular Biology Department, University of Guelph, 50 Stone Rd. E. Guelph, Ontario, Canada, N1G 2W1 (1)
Montreal Heart Institute/Institut de Cardiologie de Montréal, Université de Montréal, Montréal, QC, Canada Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada (1)
National Institute of Standards and Technology (1)
Professor of Glycobiology University of Helsinki Helsinki University central Hospital (1)
Professor of Glycobiology, University of Helsinki Helsinki University Hospital (1)
Proteome Research (AG Stühler) Institute of Molecular Medicine Heinrich Heine University Düsseldorf 40225 Düsseldorf Germany (1)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (1)
State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, P.R. China; (1)
Stress- and Immunoproteomics group, Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany (1)
The Department of Microbiology and Plant Biology,the University of Oklahoma (1)
University Medicine Greifswald (1)

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Toxoplasma gondii metabolic flexibility in response to iron deprivation

Iron is an essential nutrient for many critical cellular processes. As a consequence of diverse and dynamic host environments, the obligate intracellular parasite Toxoplasma gondii must adapt to iron limited conditions. To investigate the adaptations critical to parasite survival under these cond...

2026-03-18 | MTBLS12831 | MetaboLights

Stable isotope labelling of Toxoplasma gondii under iron and copper restriction

Toxoplasma uses metal nutrients like iron and copper for vital functions in their energy metabolism. Here, we have used stable isotope labelling to track the incorporation of glucose and glutamine into metabolic pathways, primarily focusing on central carbon metabolism, when these metals are disr...

2026-03-18 | MTBLS13492 | MetaboLights

LC-MS/MS targeted analysis of ferroptosis-associated phospholipid peroxidation in KIF11-depleted HRECs

Human retinal vascular endothelial cells (HRECs) were transfected with lentivirus encoding either KIF11-targeting shRNA or a non-targeting control. KIF11-depleted and control cells were then subjected to lipid extraction followed by LC–MS/MS–based targeted analysis of ferroptosis-associated phosp...

2026-02-13 | MTBLS12912 | MetaboLights

Transcription profiling of Bacillus anthracis Sterne during iron starvation

Effects of iron starvation on the transcriptional profile of Bacillus anthracis

ORGANISM(S): Bacillus anthracis

2010-07-22 | E-MEXP-2272 | biostudies-arrayexpress

Bordetella bronchiseptica RB50 iron limitation 2

Bordetella bronchiseptica RB50 was shifted from iron replete to either iron depleted or iron replete media, and samples were taken post shift for transcriptional profiling

ORGANISM(S): Bordetella bronchiseptica

2011-09-08 | E-MEXP-3076 | biostudies-arrayexpress

Iron regulation in P. syringae DC3000

DC3000 cultures were grown under highly controlled conditions and after the addition of iron citrate or sodium citrate to the media. In the cultures supplemented with iron, we found that cell-associated iron increased rapidly while culture densities were not significantly different over 4 hours when...

ORGANISM(S): Pseudomonas syringae pv. tomato str. DC3000

2008-11-07 | E-GEOD-13500 | biostudies-arrayexpress

Bordetella pertussis Tohama I iron limitation 1

B. pertussis Tohama I was grown in iron-depleted or iron-replete media and sampled at several time points to assess global gene expression

ORGANISM(S): Bordetella pertussis

2011-09-08 | E-MEXP-3263 | biostudies-arrayexpress

Transcriptional effect of aft1 and aft2 mutation in iron depleted conditions

The paralogous transcription factors Aft1p and Aft2p activate the expression of genes involved in iron metabolism under iron depleted conditions. Both are able to bind to the same DNA consensus sequence in vitro. We used DNA microarrays and loss of function mutant strains to better understand the re...

ORGANISM(S): Saccharomyces cerevisiae

2010-06-09 | E-GEOD-1763 | biostudies-arrayexpress

Transcription profiling of Mycobacterium tuberculosis wild type, ideR mutant and ideR complemented mutants strains grown in iron-sufficient or iron-deficient media

The mycobacterial IdeR protein is a metal-dependent regulator of the DtxR (diphtheria toxin repressor) family. In the presence of iron, it binds to a specific DNA sequence in the promoter regions of the genes that it regulates, thus controlling their transcription. In this study, we provide evidence...

ORGANISM(S): Mycobacterium tuberculosis

2007-09-12 | E-TABM-317 | biostudies-arrayexpress

Shotgun proteome analysis of Bordetella pertussis reveals a distinct influence of iron availability on the bacterial metabolism, virulence, and defense response.

Data from ProteomeXchange, PXD ID: PXD001280. File: 120313_O4_YL__Bp_Fe_1.mzml. Published as part of Proteomics. 2015 Mar 9 . From the Abstract: {{i}} One of the mechanisms involved in host immunity is the limitation of iron accessibility to pathogens, which in turn provokes the corresponding physi...

ORGANISM(S): Bordetella_pertussis_tohama_i

GPM32310018525 | GPMDB

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