By Samantha S - OmicsDI

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Genomics (54)
Transcriptomics (45)
Unknown (43)
Proteomics (33)
Metabolomics (6)
Genomic (2)
Models (1)
Other (1)

Organisms

Homo sapiens (84)
Mus musculus (13)
Saccharomyces cerevisiae (3)
Giardia lamblia ATCC 50803 (3)
Mycobacterium tuberculosis (3)
Mycobacterium tuberculosis CDC1551 (3)
Oncorhynchus mykiss (2)
Escherichia coli (2)
Porphyromonas gingivalis (1)
Schizosaccharomyces pombe (1)
Streptococcus pneumoniae (1)
Salmonella enterica subsp. enterica serovar Typhimurium (1)
Aenocyon dirus (1)
Bacteria (1)
Candida albicans (1)
Giardia duodenalis assemblage A (1)
Giardia duodenalis assemblage B (1)
Kluyveromyces marxianus DMKU3-1042 (1)
Mycolicibacterium smegmatis MC2 155 (1)
Plasmodium falciparum 3D7 (1)
Rattus norvegicus (1)
Saccharomyces kudriavzevii ZP591 (1)

Organisms

Spilogale interrupta (1)

Repository

EGA (50)
biostudies-arrayexpress (48)
pride (25)
MassIVE (8)
MetaboLights (6)
dbGaP (2)
BioModels (1)
GPMDB (1)
ENA (1)

Tissue

Trophozoite (4)
Binucleate cell (3)
Cell culture (3)
Macrophage (2)
B cell (1)
Bacterial protein (1)
Binucleate (1)
Blood plasma (1)
Blood serum (1)
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Cellular modified amino acid catabolic process (1)
Epithelial cell (1)
Pancreatic beta cell line (1)
Sensory nerve (1)
Sperm (1)
Spinal cord (1)
Spleen (1)
Sporozoite (1)

Disease

Giardiasis (5)
Tuberculosis (3)
Not Available (1)
Bone osteosarcoma (1)
Breast cancer (1)
Lymphoma (1)
Type 1 diabetes mellitus (1)

Technology Type

Mass Spectrometry (25)
Shotgun proteomics (17)
Illumina 15K (8)
Mass spectrometry (6)
Bottom-up proteomics (4)
Data-independent acquisition (4)
Data-dependent acquisition (2)
Gel-based experiment (2)
ILLUMINA, Illumina HiSeq 2000 (1)
Illumina OmniQuad 2.5 - CNVpartition (1)
Affinity purification coupled with mass spectrometry proteomics (1)
SWATH MS (1)
Top-down proteomics (1)

Instrument Platform

NextSeq 500 (5)
Illumina HiSeq 4000 (3)
Illumina NovaSeq 6000 (2)
Orbitrap Fusion Lumos (2)
Q Exactive HF (2)
Q Exactive Plus (2)
Liquid Chromatography MS - negative - reverse phase (2)
Liquid Chromatography MS - positive - reverse phase (2)
Quiagen Mini prep kit (1)
BD FACS JAZZ (1)
Axon GenePix 4000B scanning hardware (1)
HiSeq X Ten (1)
Illumina HiSeq 2500 (1)
Instrument (1)
Orbitrap Eclipse (1)
Orbitrap Exploris 480 (1)
Orbitrap Fusion (1)
Orbitrap Fusion ETD (1)
6550 Q-TOF LC-MS Agilent (1)
Flow injection analysis MS - negative (1)
Flow injection analysis MS - positive (1)
SYNAPT HDMS (Waters) (1)

Publication Date

2025 (10)
2021 (9)
2015 (8)
2010 (8)
2014 (7)
2013 (6)
2020 (6)
2022 (5)
2026 (4)
2016 (4)
2024 (4)
2023 (4)
2019 (4)
2009 (2)
2008 (2)
2018 (2)
2012 (1)
2007 (1)

CHEBI ID

CHEBI:15611 (3)
CHEBI:16865 (3)
CHEBI:16958 (3)
CHEBI:17053 (3)
CHEBI:37024 (3)
CHEBI:15318 (2)
CHEBI:15414 (2)
CHEBI:15428 (2)
CHEBI:15603 (2)
CHEBI:15727 (2)
CHEBI:15741 (2)
CHEBI:15891 (2)
CHEBI:15940 (2)
CHEBI:15956 (2)
CHEBI:15971 (2)
CHEBI:16015 (2)
CHEBI:16024 (2)
CHEBI:16027 (2)
CHEBI:16108 (2)
CHEBI:16196 (2)
CHEBI:16217 (2)
CHEBI:16235 (2)
CHEBI:16283 (2)
CHEBI:16335 (2)
CHEBI:16349 (2)
CHEBI:16410 (2)
CHEBI:16414 (2)
CHEBI:16449 (2)
CHEBI:16450 (2)
CHEBI:16467 (2)

Metabolite Name

Citric acid (3)
Hypoxanthine (3)
L-Alanine (3)
L-Isoleucine (3)
L-Leucine (3)
L-Methionine (3)
L-Phenylalanine (3)
L-Valine (3)
Pyruvate (3)
Succinic acid (3)
Uracil (3)
1-Methylnicotinamide (2)
2-Hydroxy-3-methylbutyric acid (2)
3-Methyl-2-oxovaleric acid (2)
3-Ureidopropionic acid (2)
4-Guanidinobutyric acid (2)
4-Hydroxybenzoic acid (2)
4-Hydroxyphenylacetic acid (2)
5-Methyluridine (2)
Adenine (2)
Adenosine (2)
Adenosine monophosphate (2)
Betaine (2)
Biotin (2)
Choline (2)
Cytidine (2)
D-Arabitol (2)
D-Glucose (2)
D-Mannose (2)
D-Ribose 5-phosphate (2)

IsPrivate

False (1)

Model Flag

Non Kinetic (1)

First Public Date

2022 (1)

Modelling Approach

Constraint-based model (1)

Modification

2x(15)N labeled L-lysine (1)
4x(15)N labeled L-arginine (1)

Study type

Transcription profiling by array (30)
RNA-seq of coding RNA (9)
Ribo-seq (2)
RNA-seq of total RNA (2)
Unknown experiment type (1)
Other (1)
ChIP-seq (1)
DNA-seq (1)
Methylation profiling by high throughput sequencing (1)

Release Date

2025 (12)
2015 (9)
2010 (8)
2016 (7)
2014 (7)
2013 (7)
2024 (7)
2022 (6)
2021 (6)
2023 (5)
2012 (3)
2020 (3)
2018 (3)
2009 (2)
2008 (2)
2026 (1)
2007 (1)
2019 (1)
2017 (1)

Lab affiliation

1DST/NRF Centre of Excellence in Biomedical Tuberculosis research, SA MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa (3)
DST/NRF Centre of Excellence in Biomedical Tuberculosis research, SA MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa (2)
Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town (2)
Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia (2)
1 Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia (1)
BioArCh, Department of Archaeology, University of York (1)
DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa (1)
Department of Biomedical Sciences, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa. (1)
Department of Genetics, Cell Bioliogy, & Anatomy Buckley Lab University of Nebraska Medical Center Omaha, Nebraska United States of America (1)
Drummond Lab, Genetics, Genomics, and Systems Biology, University of Chicago (1)
Genetics, Genomics, and Systems Biology, The University of Chicago (1)
George Mason University (1)
Infection and Global Health, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia. Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia. Diagnostic Haematology, The Royal Melbourne Hospital, Melbourne, Victoria, Australia. (1)
Institute of Integrative Biology University of Liverpool Crown Street, Liverpool L69 7ZB (1)
Monash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia (1)
Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia (1)
The University of Guelph, Guelph, Ontario, Canada. The department of Biomedical Sciences at the Ontario Veterinary College. (1)
University of Colorado Denver Anschutz Medical Campus, Department of Pharmaceutical Sciences, Colorado, USA (1)
University of Michigan (1)
Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia Faculty of Veterinary and Agricultural Science, University of Melbourne, Melbourne, Victoria, Australia (1)

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Discovery of A-type procyanidin dimers in yellow raspberries by untargeted metabolomics and correlation based data analysis

Introduction:Raspberries are becoming increasingly popular due to their reported health beneficial properties. Despite the presence of only trace amounts of anthocyanins yellow varieties seems to show similar or better effects in comparison to conventional raspberries.Objectives:The a...

2016-08-23 | MTBLS333 | MetaboLights

Metabolomics of Solanum lycopersicum infected by Phytophthora infestans leads to Late blight detection and reveals metabolic differences in infection times

Tomato crops suffer attacks of various pathogens that cause large production losses. Late blight caused by Phytophthora infestans is a devastating disease in tomatoes because of its difficultly to control. Here, we applied metabolomics based on liquid chromatography–mass spectrometry (LC-MS) and met...

2019-01-24 | MTBLS618 | MetaboLights

Transcriptional profiling of E. coli after addition of peroxynitrite or hydrogen peroxide to aerobically growing cells

Peroxynitrite is formed in macrophages by the diffusion-limited reaction of superoxide and nitric oxide. This highly reactive species is capable of causing both oxidative and nitrosative stress in Escherichia coli. Previous studies have focused on the reactions of peroxynitrite with specific protein...

ORGANISM(S): Escherichia coli

2010-05-24 | E-GEOD-19370 | biostudies-arrayexpress

Bioremediation of a common product of food processing by a human gut bacterium

ORGANISM(S): Mus Musculus (ncbitaxon:10090) Microbiome

2019-08-27 | MSV000084239 | MassIVE

Differential Gene Expression of Soluble CD8+ T-cell mediated suppression of HIV replication in three older children

Goal: To compare the gene expression profiles from pediatric patients with each other, with those reported in adults and in those related to exosomes. Background: Suppression of human immunodeficiency virus (HIV) replication by CD8+ T-cells (CD8 suppression) contributes to survival in adults and chi...

ORGANISM(S): Homo sapiens

2010-10-28 | E-GEOD-23183 | biostudies-arrayexpress

Analysis of Growth Phases of Enterotoxigenic Escherichia coli Reveals a Distinct Transition Phase before Entry into Early Stationary Phase with Shifts in Tryptophan, Fucose, and Putrescine Metabolism and Degradation of Neurotransmitter Precursors

Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea in children and adults in endemic areas. Gene regulation of ETEC during growth in vitro and in vivo needs to be further evaluated, and here we describe the full transcriptome and metabolome of ETEC dur...

2022-07-15 | MTBLS3540 | MetaboLights

Diet suppresses glioblastoma initiation in mice by maintaining quiescence of mutation-bearing neural stem cells.

Not available

S-EPMC10618406 | biostudies-literature

Induced membrane technique combined with antibiotic-loaded calcium sulfate-calcium phosphate composite as bone graft expander for the treatment of large infected bone defects: preliminary results of 12 cases.

Not available

S-EPMC7575946 | biostudies-literature

An adaptive biomolecular condensation response is conserved across environmentally divergent species

Cells must sense and respond to sudden maladaptive environmental changes—stresses—to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures k...

ORGANISM(S): Saccharomyces kudriavzevii ZP591 Kluyveromyces marxianus DMKU3-1042 Saccharomyces cerevisiae (Baker's yeast)

2024-03-03 | PXD044970 | Pride

Trancription profiling of the hepatoma cell line Huh7 infected with the Hepatitis C Virus

Hepatitis C Virus is a leading cause of chronic liver disease. The identification and characterisation of key host cellular factors that play a role in the HCV replication cycle is important for the understanding of disease pathogenesis and the identification of novel anti-viral therapeutic targets....

ORGANISM(S): Homo sapiens

2010-05-27 | E-GEOD-20948 | biostudies-arrayexpress

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185 Results

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