Jones F F - OmicsDI

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Unknown (6184)
Genomics (174)
Transcriptomics (148)
Proteomics (91)
Metabolomics (35)
Models (2)
Genomic (2)
Multiomics (2)

Organisms

Homo sapiens (257)
Mus musculus (36)
Arabidopsis thaliana (14)
Caenorhabditis elegans (13)
Rattus norvegicus (8)
Drosophila melanogaster (7)
Saccharomyces cerevisiae (7)
Chlorocebus aethiops (6)
Nicotiana tabacum (4)
Streptococcus pneumoniae (3)
Ginkgo biloba (2)
Taeniopygia guttata (2)
Lepeophtheirus salmonis (2)
Biomphalaria glabrata (2)
Bombus terrestris (2)
Human immunodeficiency virus 1 (2)
Fusarium oxysporum f. sp. niveum (1)
Cimex lectularius (1)
Phytophthora sojae (1)
Populus trichocarpa x Populus deltoides (1)
Macaca mulatta (1)
Francisella tularensis (1)
Bacillus subtilis (1)
Aedes aegypti (1)
Staphylococcus aureus (1)
Ovis aries (1)
Triticum aestivum (1)
Escherichia coli str. K-12 substr. MG1655 (1)
Clostridium acetobutylicum ATCC 824 (1)
572307 (1)

Organisms

Amycolatopsis sp. BJA-103 (2)
Dendroctonus ponderosae (2)
Escherichia coli str. K-12 substr. MG1655 (1)
Saccharomyces cerevisiae (1)

Repository

biostudies-arrayexpress (169)
EGA (136)
pride (77)
MetaboLights (34)
ENA (17)
MassIVE (9)
PanoramaPublic (3)
BioModels (2)
dbGaP (2)
PAXDB (2)
GNPS (1)

Tissue

Cell culture (18)
Permanent cell line cell (10)
Blood plasma (4)
Brain (4)
Epithelial cell (4)
Colon (3)
Kidney (3)
Liver (3)
Lung (3)
T cell (3)
Blood serum (2)
Enterocyte (2)
Fibroblast (2)
Hepatocyte (2)
Intestine (2)
Keratinocyte (2)
Plant cell (2)
Skin (2)
Adipose tissue (1)
Astrocyte (1)
Bile (1)
Bile duct (1)
Blood (1)
Blood cell (1)
Blood-lymph (1)
Bone marrow (1)
Cardiomyocyte cell line (1)
Cecum (1)
Cell suspension culture (1)
T-lymphocyte cell line (1)

Disease

Severe acute respiratory syndrome (8)
Colon cancer (3)
Neuroblastoma (3)
Normal (2)
Acute leukemia (2)
Brain cancer (2)
Salmonella infectious disease (2)
Perilobar nephrogenic rest (1)
S. mansoni - exposed (1)
None (1)
Schistosome-exposed (1)
Central nervous system cancer (1)
Wilms tumour (1)
Breast cancer (1)
Brain glioblastoma multiforme (1)
Childhood extraosseous osteosarcoma (1)
Cholangiocarcinoma (1)
Chronic bronchitis (1)
Crohn's disease (1)
Embryonal rhabdomyosarcoma (1)
Fibrosarcoma (1)
Head and neck cancer (1)
Inflammation (1)
Liver cancer (1)
Low grade glioma (1)
Lung carcinoma (1)
Malignant mesothelioma (1)
Malignant neoplasm of ovary (1)
Melanoma (1)
Osteosarcoma (1)

Technology Type

Mass Spectrometry (77)
Shotgun proteomics (51)
Mass spectrometry (28)
Bottom-up proteomics (11)
Illumina 15K (8)
Affinity purification coupled with mass spectrometry proteomics (8)
NMR spectroscopy (4)
Data-dependent acquisition (4)
Data-independent acquisition (4)
Illumina HiSeq 2000 (3)
Gel-based experiment (3)
HDMSE (3)
SWATH MS (3)
Top-down proteomics (3)
Mass spectrometry assay (2)
Chemical cross-linking coupled with mass spectrometry proteomics (2)
AB SOLiD 4 System, Illumina HiSeq 2500, Illumina HiSeq 2000, AB SOLiD System 3.0 (1)
ABI_SOLID, Illumina Genome Analyzer IIx, Affymetrix_GenomeWide_SNP6.34 (1)
Illumina 610K Quad, Illumina 1.2M (1)
Illumina Genome Analyzer II (1)
Illumina HiSeq 2000, Illumina Genome Analyzer IIx (1)
Illumina HiSeq 2500 (1)
Illumina HiSeq 2500 (ILLUMINA), AB SOLiD System (ABI_SOLID) (1)
Illumina Human 1.2M Duo custom BeadChips v1 - Genome Studio, Illumina Human 660K Quad BeadChips - Illuminus, Illumina Human-Ref 8 v3.0 expression array (1)
Illumina Infinium HumanMethylation450 BeadChips (1)
Life Tech - Solid (1)

Instrument Platform

Liquid Chromatography MS - positive - reverse phase (10)
Liquid Chromatography MS - negative - reverse phase (9)
Liquid Chromatography MS - positive - hilic (7)
Liquid Chromatography MS - negative - hilic (5)
GenePix Professional 4200A [Axon Instruments] (3)
5975C Series GC/MSD (Agilent) (3)
Nuclear Magnetic Resonance (NMR) - (3)
Illumina NovaSeq 6000 (2)
Illumina HiSeq 2000 (2)
LTQ Orbitrap Elite (2)
Orbitrap Eclipse (2)
Direct infusion MS - negative (2)
Gas Chromatography MS - (2)
Liquid Chromatography MS - (2)
Liquid Chromatography MS - Positive (LC-MS (Positive)) (2)
Illumina-compatible library preparation equipment (1)
Monarch RNA purification column system (1)
Standard mammalian cell culture equipment (1)
Illumina NovaSeq X (1)
Illumina HiSeq 2500 (1)
Illumina HiSeq 4000 (1)
NextSeq 500 (1)
Q Exactive Plus (1)
LTQ Orbitrap (1)
Orbitrap Fusion (1)
Q Exactive HF-X (1)
SolariX (1)
TripleTOF 6600 (1)
ZenoTOF 7600 (1)
Bruker (1)

Publication Date

2013 (27)
2014 (25)
2012 (25)
2021 (22)
2015 (21)
2010 (17)
2011 (16)
2022 (16)
2023 (15)
2025 (14)
2009 (14)
2016 (12)
2008 (12)
2024 (10)
2020 (10)
2019 (9)
2026 (7)
2018 (7)
2017 (6)
2006 (4)
2007 (3)
2004 (1)

UNIPROT ID/AC

10090.ENSMUSP00000072775 (2)
10090.ENSMUSP00000079944 (2)
10090.ENSMUSP00000105709 (2)
10090.ENSMUSP00000117461 (2)
10090.ENSMUSP00000127198 (2)
10090.ENSMUSP00000132065 (2)
10090.ENSMUSP00000132102 (2)
10090.ENSMUSP00000136357 (2)
10090.ENSMUSP00000136375 (2)
10090.ENSMUSP00000136544 (2)
10090.ENSMUSP00000137171 (2)
10090.ENSMUSP00000137236 (2)
1433B_MOUSE (2)
1433E_MOUSE (2)
1433Z_MOUSE (2)
2AAA_MOUSE (2)
3BHS1_MOUSE (2)
3HIDH_MOUSE (2)
4F2_MOUSE (2)
6PGD_MOUSE (2)
6PGL_MOUSE (2)
P00451 (1)
P00734 (1)
P00740 (1)
P00742 (1)
P01008 (1)
P08709 (1)
P10646 (1)
P12259 (1)
P13726 (1)

CHEBI ID

CHEBI:16335 (9)
CHEBI:16737 (9)
CHEBI:30769 (9)
CHEBI:15354 (8)
CHEBI:15428 (8)
CHEBI:17368 (8)
CHEBI:25094 (8)
CHEBI:32816 (8)
CHEBI:15756 (7)
CHEBI:15971 (7)
CHEBI:17568 (7)
CHEBI:17750 (7)
CHEBI:25017 (7)
CHEBI:28300 (7)
CHEBI:15741 (6)
CHEBI:16015 (6)
CHEBI:16199 (6)
CHEBI:16708 (6)
CHEBI:16919 (6)
CHEBI:17126 (6)
CHEBI:17596 (6)
CHEBI:17748 (6)
CHEBI:17754 (6)
CHEBI:18186 (6)
CHEBI:22653 (6)
CHEBI:16040 (5)
CHEBI:16196 (5)
CHEBI:16634 (5)
CHEBI:16704 (5)
CHEBI:16977 (5)

Metabolite Name

Glycine (7)
Urea (7)
Adenosine (5)
Creatinine (5)
Hypoxanthine (5)
Pyruvic acid (5)
Succinic acid (5)
Tyrosine (5)
Uracil (5)
Adenine (4)
Alanine (4)
Citric acid (4)
Citric acid (4)
Creatinine (4)
Fructose (4)
Fumaric acid (4)
Glutamine (4)
Glyceric acid (4)
Glycerol (4)
Isoleucine (4)
L-histidine (4)
Leucine (4)
Phenylalanine (4)
Proline (4)
Putrescine (4)
Taurine (4)
Valine (4)
Xanthine (4)
Betaine (3)
Choline (3)

First Public Date

2017 (10)
2021 (2)
2025 (1)
2023 (1)
2019 (1)
2014 (1)
2013 (1)

Modelling Approach

Constraint-based model (1)
Ordinary differential equation model (1)

Lab affiliation

Centre for Proteome Research, University of Liverpool, Liverpool, UK (9)
Forensic Science Center, Lawrence Livermore National Laboratory (2)
Institute of Integrative Biology, University of Liverpool (2)
Sequence database group (2)
University of Warwick (2)
Wellcome Trust Sanger Institute (2)
Alzheimer’s Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, U.K. (1)
Associate Professor Systems Virology Department of Translation medicine Faculty of Medicine Lund University Sweden (1)
BCI Mass spectrometry Facility 1.02 & 1.03 1st floor Barts Cancer Institute Queen Mary, University of London John Vane Science Centre, Charterhouse Square, London EC1M 6BQ (1)
Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada (1)
Centre for Proteomic Research, University of Southampton (1)
Chair in Infection and Global Health, Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, UK (1)
Department of Anatomy and Cell Biology, Faculty of medecine and Health Sciences, Université de Sherbrooke (1)
Department of Anatomy and Cell Biology, Université de Sherbrooke (1)
Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA (1)
Department of Biochemistry and Microbiology, L-Probe Lab Ghent University (1)
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA (1)
Department of Biological Sciences University of Alberta G-504 Biological Sciences Bldg. Edmonton Alberta T6G 2E9 Canada (1)
Department of Biology, University of Crete, Heraklion, Greece Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsaala, Sweden (1)
Department of Biology, University of Crete, Heraklion, Greece Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology- Hellas, Heraklion, Greece Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden (1)
Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University (1)
Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada (1)
Director of PEL @ Caltech (1)
Discovery Proteomics Facility, Oxford (1)
EMBL Grenoble (1)
ExxonMobil Research and Engineering Company (1)
Full Professor of Paediatric Molecular Haemato-Oncology School of Medicine,University College Dublin, School of Medicine, Systems Biology Ireland Temple Street Dublin 1 (1)
Head of the Curie Institute Mass Spectrometry Platform (1)
Icahn School of Medicine at Mount Sinai (1)
Institute for Medical Virology, University of Zurich (1)

IsPrivate

False (2)

Model Flag

Non Kinetic (1)

Classification

bacteria (1)

Modification

Not available (1)

Study type

Transcription profiling by array (90)
ChIP-seq (21)
RNA-seq of coding RNA (17)
Comparative genomic hybridization by array (10)
Unknown experiment type (7)
Methylation profiling by array (5)
ChIP-chip by tiling array (3)
Genotyping by array (3)
RNA-seq of non coding RNA (3)
Other (2)
Transcription profiling by high throughput sequencing (1)
Animal - One-color microarray (1)
One-color microarray (1)
Human - One-color microarray (1)
Cell line - High-throughput sequencing (1)
Transcription profiling by tiling array (1)
ATAC-seq (1)
RNA-seq of coding RNA from single cells (1)

Release Date

2022 (705)
2021 (681)
2023 (592)
2025 (569)
2020 (538)
2024 (533)
2018 (379)
2019 (366)
2015 (275)
2016 (269)
2017 (267)
2014 (239)
2012 (168)
2013 (166)
2011 (149)
2010 (106)
2026 (92)
2009 (85)
2008 (61)
2007 (42)
2006 (26)
2005 (17)
2004 (7)
2003 (6)
2002 (4)
2001 (4)
2000 (4)
1998 (2)
1999 (1)

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microRNA-like RNAs exploring and expression profile in plant pathogenic fungus Fusarium oxysporum f. sp. niveum

To explore the presence of milRNA in Fusarium oxysporum f. sp. niveum (Fon) and evaluate their expression at different propagules, two categories of sRNAs were identified from Fon hyphae and microconidia by using illumina sequencing. A total of 650,960 and 561,114 unique sRNAs were obtained from the...

ORGANISM(S): Fusarium oxysporum f. sp. niveum

2016-07-15 | E-GEOD-84384 | biostudies-arrayexpress

TFT3 interacts with MAPKKK by coimmunoprecipitation

Tomato MAPKKK interacts with the N. benthamiana homologue of TFT3. MAPKKK-HA was transiently expressed in N. benthamiana leaves and immunoprecipitated using -HA agarose beads. 12 unique peptides of N. benthamiana TFT3 homologue were identified by liquid chromatography–mass spectrometry.

ORGANISM(S): Nicotiana tabacum (Common tobacco)

2023-05-10 | PXD041469 | Pride

Tomato Plant defecnce

Metabolic Profiling of Volatile Organic Compounds (VOCs) Emitted by the Pathogens Francisella tularensis and Bacillus anthracis in Liquid Culture

We conducted comprehensive (untargeted) metabolic profiling of volatile organic compounds (VOCs) emitted in culture by bacterial taxa Francisella tularensis (F. tularensis) subspecies novicida and Bacillus anthracis (B. anthracis) Sterne, surrogates for potential bacterial bioterrorism agents, as we...

2020-08-20 | MTBLS1737 | MetaboLights

Global identification of yeast chromosome interactions using genome conformation capture

The objective of this study was to determine the global chromosomal interaction map for exponentially growing Saccharomyces cerevisiae cells using Genome Conformation Capture. Interactions between chromosomes were identified within a population of yeast cells growing exponentially in a semi-defined ...

ORGANISM(S): Saccharomyces cerevisiae

2009-07-21 | E-GEOD-13648 | biostudies-arrayexpress

Positron Emission Tomography Imaging of Staphylococcus aureus Infection Using a Nitro-Prodrug Analogue of 2-[¹⁸F]F-p-Aminobenzoic Acid.

Not available

S-EPMC7429255 | biostudies-literature

In vitro effect of the integrine LAMA4 on motility and cluster formation of human chondrocytes

Background: Cluster formation of hypertrophic chondrocytes is a sign of late stage osteoarthritis. In vitro chondrocytes have the ability to migrate on scaffolds. Important for motility issues in cartilage are integrines, part of the extracellular matrix, important for locomotory stimuli. The integr...

ORGANISM(S): Homo sapiens

2015-12-22 | E-GEOD-68428 | biostudies-arrayexpress

Positron Emission Tomography Imaging with 2-[¹⁸F]F- p-Aminobenzoic Acid Detects Staphylococcus aureus Infections and Monitors Drug Response.

Not available

S-EPMC6226330 | biostudies-literature

F-actin homeostasis through transcriptional regulation and proteasome-mediated proteolysis.

Not available

S-EPMC6048543 | biostudies-literature

Molecular Dynamics Study of Wetting and Adsorption of Binary Mixtures of the Lennard-Jones Truncated and Shifted Fluid on a Planar Wall.

Not available

S-EPMC8280723 | biostudies-literature

Alternative conformations of a major antigenic site on RSV F.