E.coli - OmicsDI

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Genomics (1300)
Unknown (713)
Transcriptomics (474)
Proteomics (363)
Metabolomics (32)
Other (12)
Models (10)
Methylation profiling (1)

Organisms

Escherichia coli (196)
Homo sapiens (84)
Mus musculus (79)
Escherichia coli str. K-12 substr. MG1655 (37)
Caenorhabditis elegans (24)
Drosophila melanogaster (15)
Escherichia coli K-12 (14)
Gallus gallus (11)
Saccharomyces cerevisiae (11)
Rattus norvegicus (8)
Bos taurus (8)
Escherichia coli CFT073 (8)
Escherichia coli O157:H7 str. Sakai (7)
Sus scrofa (6)
Hordeum vulgare (5)
Escherichia coli O157:H7 (5)
Klebsiella pneumoniae (4)
Escherichia coli str. K-12 substr. W3110 (4)
Prochlorococcus marinus subsp. pastoris str. CCMP1986 (3)
synthetic construct (3)
Arabidopsis thaliana (3)
human gut metagenome (2)
Escherichia coli O55:H7 (2)
Escherichia coli SE15 (2)
Papio cynocephalus (2)
Bordetella sp. IITR-02 (2)
Pectobacterium atrosepticum SCRI1043 (1)
Eggerthella lenta DSM 2243 (1)
Escherichia coli DH1 (1)
Petrolisthes cinctipes (1)

Organisms

Escherichia coli (458)
Mus musculus (44)
Escherichia coli str. K-12 substr. MG1655 (29)
Homo sapiens (27)
Escherichia coli K-12 (15)
Caenorhabditis elegans (11)
Sus scrofa (9)
Dictyostelium discoideum (6)
Escherichia coli BW25113 (5)
Pseudomonas fluorescens (5)
Ovis aries (5)
Escherichia coli str. K-12 substr. W3110 (3)
Escherichia coli O157:H7 (3)
Danio rerio (3)
Saccharomyces cerevisiae (3)
Bacteria (3)
Escherichia phage vB_EcoM_ECP26 (2)
Teseptimavirus T7 (2)
Periplaneta americana (2)
Escherichia coli DH5[alpha] (2)
Escherichia coli BL21 (2)
Escherichia coli MC1061 (2)
Escherichia coli LF82 (2)
Pseudomonas aeruginosa PAO1 (2)
Drosophila melanogaster (2)
sediment metagenome (2)
Gallus gallus (2)
Klebsiella pneumoniae (2)
Escherichia coli TW11681 (1)
Escherichia coli IS1 (1)

Repository

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biostudies-arrayexpress (364)
pride (285)
geo (153)
MassIVE (30)
iProX (23)
PAXDB (19)
GNPS (15)
MetaboLights (9)
MetabolomicsWorkbench (8)
BioModels (7)
jPOST (5)
EGA (3)
FAIRDOMHub (3)
GPMDB (1)
NODE (1)

Tissue

Cell culture (57)
Permanent cell line cell (8)
Cell suspension culture (7)
Blood plasma (7)
Whole body (6)
Blood serum (5)
Epithelial cell (5)
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Brain (4)
Cell line cell (4)
Cells (3)
Macrophage (3)
Cerebrospinal fluid (2)
Prokaryotic cell (2)
Lung (2)
Blood cell (2)
T cell (2)
Blood (2)
Feces (1)
Meyloid lineage cells (1)
HAP-1 cell (1)
Brainstem motor neuron (1)
K-562 cell (1)
Bacteriocyte (1)
Brain microvascular endothelial cell (1)
Pancreatic islet cell (1)
Head (1)
Neuroblast (1)
Fruit (1)
Pancreatic ductal cell (1)

Disease

Normal (9)
Pancreatic cancer (3)
Disease free (3)
Squamous cell carcinoma (2)
Obesity (2)
Amyotrophic lateral sclerosis (2)
Unspecified peripheral T-cell lymphoma (1)
Oropharynx squamous-cell carcinoma in DiseaseLocation oropharynx has DiseaseStaging lymph node negative (N0) (1)
Embryonic lethal at day 8.5 to 9.5 (1)
Blumeria graminis hordei (powdery mildew) inoculation (1)
Hypertension (1)
Severe acute respiratory syndrome (1)
Hodgkin lymphoma, mixed cellularity, stage IV (1)
Infected (1)
IBDV infected (1)
Barrett's esophagus (1)
Reference (1)
Glioblastoma (1)
Non infected (1)
H9N2 infected (1)
Not Available (1)
Retinal detachment (1)
Connective tissue disease (1)
Bacterial meningitis (1)
Oral squamous cell carcinoma (1)
Legionellosis (1)
Oropharynx cancer (1)
Prostate adenocarcinoma (1)
Mixed disorder as reaction to stress (1)
Neuroblastoma (1)

Technology Type

Mass Spectrometry (293)
Shotgun proteomics (150)
Bottom-up proteomics (54)
Data-independent acquisition (25)
Data-dependent acquisition (22)
Chemical cross-linking coupled with mass spectrometry proteomics (18)
Top-down proteomics (16)
Affinity purification coupled with mass spectrometry proteomics (16)
SWATH MS (14)
Gel-based experiment (14)
Mass spectrometry (7)
ESI (6)
MSE (4)
HDMSE (4)
SRM/MRM (4)
Mass spectrometry assay (2)
EI (2)
DiaPASEF (2)
All-ion fragmentation (1)

Instrument Platform

Illumina HiSeq 2500 (6)
G2565AA DNA microarray scanner [Agilent] (5)
Illumina NovaSeq 6000 (5)
NextSeq 500 (5)
G2565BA DNA microarray scanner [Agilent] (4)
Illumina HiSeq 2000 (3)
. (2)
GenePix 4000A [Axon Instruments] (2)
BAS-5000 [FUJIFILM] (2)
GenePix 4000B [Axon Instruments] (2)
Illumina MiSeq (2)
Desktop (1)
Bacteriological Laboratory (1)
Quantseq FWD kit (Lexogen, Austria) was used to prepare libraries for NGS. Reverse transcription of RNA, amplification of libraries, quality control of libraries and purification were performed exactly as described in manual provided with kit. (1)
RNAeasy kit (1)
Cell culture lab (1)
Illumina HiSeq 4000 system (1)
GeneChip Scanner 2500 (1)
Flow Chamber infection model (1)
BIONEER gDNA extraction kit (1)
Of TruSeq DNA Nano Sample Preparation Kit(Illumina) (1)
Illumina TruSeq Stranded mRNA Sample Prep Kit (1)
NucleoSpin RNA kit (MACHEREY-NAGEL, Germany) (1)
Retsch MM400 (1)
Axon GenePix 4000A scanning hardware (1)
Agilent scanner (1)
Affymetrix GeneChip Scanner 3000 7G (1)
G2565CA DNA microarray scanner (Agilent) for scanning. (1)
Chamber type: SureHyb hybridization chamber (Agilent). (1)
ScanArray 4000 [PerkinElmer] (1)

Publication Date

2024 (66)
2025 (55)
2014 (55)
2022 (54)
2011 (54)
2023 (53)
2010 (51)
2020 (48)
2013 (46)
2012 (45)
2021 (42)
2016 (41)
2009 (39)
2015 (37)
2026 (37)
2019 (36)
2008 (33)
2007 (29)
2017 (25)
2018 (25)
2006 (12)
2005 (10)
2004 (4)

UNIPROT ID/AC

P0A6P9 (3)
P37689 (3)
P0A799 (3)
P0A9B2 (3)
P0A858 (3)
P0A6T1 (3)
P04391 (2)
P0A786 (2)
P0A7F3 (2)
P28903 (2)
P0A9N8 (2)
P22255 (2)
P0A7D4 (2)
P39286 (2)
P0A8K1 (2)
P31120 (2)
P14407 (2)
P0AEN1 (2)
P0A6E4 (2)
P37351 (2)
P0AAB4 (2)
P0ABQ2 (2)
P0AE22 (2)
P25665 (2)
P23524 (2)
P04693 (2)
P0A6K1 (2)
P0AGF6 (2)
P0A6B4 (2)
P27838 (2)

CHEBI ID

CHEBI:58189 (3)
CHEBI:58702 (3)
CHEBI:58289 (3)
CHEBI:58272 (3)
CHEBI:57604 (3)
CHEBI:58027 (3)
CHEBI:57642 (3)
CHEBI:30616 (3)
CHEBI:61548 (3)
CHEBI:57540 (3)
CHEBI:57945 (3)
CHEBI:43474 (3)
CHEBI:456215 (3)
CHEBI:456216 (3)
CHEBI:15361 (3)
CHEBI:18291 (2)
CHEBI:18151 (2)
CHEBI:58405 (2)
CHEBI:58551 (2)
CHEBI:58271 (2)
CHEBI:16064 (2)
CHEBI:28694 (2)
CHEBI:27638 (2)
CHEBI:57262 (2)
CHEBI:28112 (2)
CHEBI:18248 (2)
CHEBI:58510 (2)
CHEBI:21437 (2)
CHEBI:1617 (2)
CHEBI:57693 (2)

Metabolite Name

Alanine (3)
Glutamine (3)
Pseudaminic acid (2)
Dihydrostreptomycin (2)
Oseltamivir phosphate (2)
CPX (2)
SB 206553 (2)
6-Acetyl-D-glucose (2)
Polhovolide (2)
D-Glucono-1,5-lactone (2)
4-Carboxy-4'-sulfoazobenzene (2)
D-Ribose 5-diphosphate (2)
3,5-Dinitrosalicylic acid (2)
UDP-glucose (2)
2,4-Bis(acetamido)-2,4,6-trideoxy-beta-L-altropyranose (2)
Tetracosanoic acid (2)
Cucurbic acid (2)
Glutamate (2)
2-C-Methyl-D-erythritol 4-phosphate (2)
Pyruvic acid (2)
Citric acid (2)
Succinic acid (2)
Leucine (2)
D-Erythrose 4-phosphate (2)
Biliverdin (2)
L-Tyrosine (2)
UDP-N-acetyl-alpha-D-glucosamine (2)
Citric acid (2)
Arginine (2)
Lysine (2)

First Public Date

2024 (230)
2013 (133)
2022 (124)
2020 (105)
2014 (103)
2018 (94)
2019 (90)
2025 (77)
2023 (74)
2021 (62)
2026 (53)
2017 (52)
2016 (35)
2015 (34)
2012 (2)
2010 (2)

Modelling Approach

Ordinary differential equation model (5)
Computational model (1)

Lab affiliation

Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany (7)
Professor, Deputy Head of Centre Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen, DENMARK (6)
Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720 (5)
Chair of Molecular Biology Institute of Cellular and Molecular Biology Estonia (4)
Forschungszentrum Juelich ZEA-3 Analytics Wilhelm-Johnen-Str D-52425 Juelich Germany (3)
University at buffalo, SUNY (3)
University Clinic for Poultry and Fish Medicine, University of Veterinary Medicine, Vienna, Austria (3)
University of Washington (3)
Department of Biochemistry and Department of Metabolic Medicine of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China (2)
Albert-Ludwigs-Universität Freiburg, Institut für Biologie III, Schänzlestr. 1, 79104 Freiburg, Germany (2)
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 (2)
Centre for Blood Research, University of British Columbia (2)
Biozentrum, University of Basel, 4056 Basel, Switzerland (2)
College of Chemistry and Molecular Engineering, Peking University, Beijing, China. (2)
Institute for Infectious Diseases, University of Bern, Switzerland (2)
Associate professor, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) (2)
Abbvie Bioresearch Center (2)
University of Louisville, Department of Chemistry, Louisville, KY 40208, USA (2)
Max Planck Institute for Terrestrial Microbiology Marburg Germany (2)
EMBL Grenoble (2)
Max Planck Institute for terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany (2)
University of Washington Department of Chemistry (2)
The Institute of Cancer Research, London (2)
Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic (2)
Jinan University (2)
State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China (2)
Michigan State University (2)
Systems Biology Ireland, University College Dublin (2)
SMBP (1)
Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria (1)

IsPrivate

False (7)

Model Flag

Non Kinetic (1)

Submitter Keywords

Ersilia (1)
Machine Learning Model (1)

Classification

bacteria (675)
viruses (11)
protozoa (7)

Modification

0.984016 (2)
42.010565 (2)
15.994915 (2)
2x(15)N labeled L-lysine (2)
4 (2)
4x(15)N labeled L-arginine (2)
57.021464 (2)
Not available (1)

Study type

Transcription profiling by array (241)
RNA-seq of coding RNA (51)
ChIP-chip by array (12)
ChIP-seq (11)
Unknown experiment type (5)
Comparative genomic hybridization by array (5)
Other (5)
Proteomic profiling by array (4)
DNA-seq (3)
RNA-seq of coding RNA from single cells (3)
ChIP-chip by tiling array (2)
Transcription profiling by tiling array (2)
RNAi profiling by array (2)
CUT&RUN (2)
Methylation profiling by high throughput sequencing (2)
One-color microarray (1)
High-throughput sequencing (1)
Animal - High-throughput sequencing (1)
Genotyping by array (1)
CLIP-seq (1)
Bisulfite-seq (1)
RIP-seq (1)
Genotyping by high throughput sequencing (1)
RNA-seq of total RNA (1)
RNA-seq of non coding RNA (1)

Release Date

2022 (76)
2014 (66)
2025 (61)
2016 (61)
2011 (58)
2023 (56)
2015 (55)
2020 (53)
2013 (51)
2012 (51)
2010 (50)
2021 (49)
2024 (46)
2019 (41)
2018 (41)
2009 (37)
2017 (34)
2008 (31)
2007 (29)
2006 (29)
2005 (29)
2003 (20)
2004 (18)
2001 (15)
2002 (12)
2000 (5)
2026 (2)
1998 (1)

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Gut microflora alleviate immune response during E.coli-induced bladder cystits via AhR/MANF activation

In recent years, with the deepening of research on intestinal microbiota, we found intestinal microbiota plays an important role in host immune regulation and barrier maintenance through cross-talk between the microbiota and the host. New evidence suggests that disruption of the fragile balance w...

2023-07-11 | MTBLS5572 | MetaboLights

E.coli K-12 treated by IPL_analysis of organic phase

Not available

ORGANISM(S): Escherichia coli

ST001657 | MetabolomicsWorkbench

Development of a weaned pig model of enterotoxigenic E.coli-induced environmental enteropathy

Not available

ORGANISM(S): Sus scrofa

ST001041 | MetabolomicsWorkbench

E.coli K-12 treated by IPL - analysis of polar phase (part-II)

Not available

ORGANISM(S): Escherichia coli