Sims J J - OmicsDI

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Unknown (1075)
Proteomics (67)
Metabolomics (62)
Transcriptomics (30)
Genomics (15)
Models (1)
Other (1)
Multiomics (1)

Organisms

Homo sapiens (37)
Mus musculus (15)
Saccharomyces cerevisiae (5)
Drosophila melanogaster (2)
Chordata (1)
Arachis hypogaea (1)
Macaca mulatta (1)
Zea mays (1)
Danio rerio (1)
Penaeus (1)

Repository

GNPS (49)
MassIVE (49)
biostudies-arrayexpress (31)
pride (18)
EGA (14)
MetaboLights (13)
BioModels (1)
GPMDB (1)
LINCS (1)

Tissue

Cell culture (3)
Fibroblast (2)
Blood (1)
Blood cell (1)
Blood plasma (1)
Brain (1)
Breast cancer cell (1)
Early embryonic cell (1)
Epithelial cell (1)
HEK-293T cell (1)
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Monocyte (1)
Muscle (1)
Neutrophil (1)
Osteoblast (1)
Permanent cell line cell (1)
Platelet (1)
Tail (1)
Testis (1)
Tibia (1)
Whole body (1)

Disease

Gray platelet syndrome (2)
Osteoarthritis (1)
Osteoporosis (1)
Paget's disease of bone (1)
Multiple sclerosis (1)
Not Available (1)
Breast cancer (1)
Glioblastoma (1)
Ovarian serous carcinoma (1)
Parkinson's disease (1)

Technology Type

Mass Spectrometry (18)
Mass spectrometry (11)
Shotgun proteomics (10)
Illumina 15K (8)
Bottom-up proteomics (5)
Mass spectrometry assay (2)
SWATH MS (2)
Fluorescence imaging (1)
Fluorescence intensity (1)
Affinity purification coupled with mass spectrometry proteomics (1)
Data-dependent acquisition (1)

Instrument Platform

LTQ Orbitrap Velos (46)
GC-MS (21)
GC MS (12)
LTQ Orbitrap (6)
Liquid Chromatography MS - positive - reverse phase (6)
AB SOLiD 4 System (3)
Illumina NovaSeq 6000 (2)
Illumina HiSeq 2000 (2)
Agilent 7890A GC with 5975C inert XL MSD (2)
Liquid Chromatography MS - negative - hilic (2)
Linux Bash Scripting (1)
NEBNext Ultra II Directional RNA Library Prep (1)
Qiagen RNeasy Mini Kit (1)
With L-glutamine supplemented with 10% fetal bovine serum (FBS) (Gibco) and 1% penicillin-streptomycin (10,000 units/mL penicillin and 10 mg/mL streptomycin) (Gibco). (1)
R (1)
Illumina HiSeq 2500 (1)
6110 Quadrupole LC/MS (1)
Agilent GC-MS (1)
LTQ FT (1)
LTQ Orbitrap Velos Pro (1)
MaXis (1)
Instrument (1)
Agilent GC/MSD 5975C (1)
Exactive (1)
LTQ Velos (1)
Orbitrap Exploris 480 (1)
Q Exactive (1)
Q Exactive HF-X (1)
Q Exactive Plus (1)
ZenoTOF 7600 (1)

Publication Date

2016 (42)
2015 (20)
2017 (18)
2023 (14)
2018 (13)
2019 (10)
2025 (7)
2022 (7)
2011 (5)
2014 (4)
2024 (3)
2021 (3)
2020 (3)
2013 (3)
2010 (2)
2026 (2)
2012 (1)
2008 (1)
2007 (1)
2006 (1)

CHEBI ID

CHEBI:16359 (3)
CHEBI:28865 (3)
CHEBI:35038 (3)
CHEBI:64563 (3)
CHEBI:139138 (2)
CHEBI:143745 (2)
CHEBI:143757 (2)
CHEBI:16027 (2)
CHEBI:16811 (2)
CHEBI:16856 (2)
CHEBI:173703 (2)
CHEBI:17858 (2)
CHEBI:182784 (2)
CHEBI:195271 (2)
CHEBI:27432 (2)
CHEBI:27997 (2)
CHEBI:29016 (2)
CHEBI:30769 (2)
CHEBI:34494 (2)
CHEBI:34687 (2)
CHEBI:64489 (2)
CHEBI:64525 (2)
CHEBI:73024 (2)
CHEBI:73858 (2)
CHEBI:75342 (2)
CHEBI:80774 (2)
CHEBI:10136 (1)
CHEBI:116314 (1)
CHEBI:131342 (1)
CHEBI:131440 (1)

Metabolite Name

Cholic acid (3)
Tris(2-butoxyethyl) phosphate (3)
(2S,3S,4S,5R,6R)-6-[[(3S,4S,6aR,6bS,8aR,9R,12aS,14bR)-9-hydroxy-4-(hydroxymethyl)-4,6a,6b,8a,11,11,14b-heptamethyl-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-yl]oxy]-5-[(2S,3R,4S,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl]oxy-3,4-dihydroxyoxane-2-carboxylic acid (2)
1-({[2-(2-furylmethyl)-5-methylpyrrolidinyl]amino}methylene)-7-[8-({[2-(2-fury lmethyl)pyrrolidinyl]amino}methylene)-1,6-dihydroxy-3-methyl-5-(methylethyl)-7 -oxo(2-naphthyl)]-3,8-dihydroxy-6-methyl-4-(methylethyl)naphthalen-2-one (2)
1-Stearoyl-2-hydroxy-sn-glycero-3-phosphocholine (2)
2,6-Di-tert-butyl-4-hydroxymethylphenol (2)
9(10)-EpOME (2)
Alpha-linolenic acid|linolenic acid|(9Z,12Z,15Z)-octadeca-9,12,15-trienoic acid (2)
Dibutyl phthalate (DBP) (2)
Elaidic acid (2)
Lyso-PC(16:0) (2)
Methionine (2)
Monoolein (2)
NCGC00385123-01_C22H30O6_7b,9-Dihydroxy-3-(hydroxymethyl)-1,1,6,8-tetramethyl-5-oxo-1,1a,1b,4,4a,5,7a,7b,8,9-decahydro-9aH-cyclopropa[3,4]benzo[1,2-e]azulen-9a-yl acetate (2)
PC(14:0/14:0) (2)
PC(16:1/16:1) (2)
PC(16:1/18:2) (2)
Succinate (2)
Taurocholic acid (2)
(R)-4-((3R,4R,5S,8S,9S,10R,13R,14S,17R)-3,4-dihydroxy-10,13-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-17-yl)pentanoic acid (1)
(R)-4-((3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-3,7,12-trihydroxy-10,13-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-17-yl)pentanoic acid (1)
1,3,5-triprop-2-enyl-1,3,5-triazaperhydroine-2,4,6-trione (1)
1,4a-dimethyl-9-oxo-7-propan-2-yl-3,4,10,10a-tetrahydro-2H-phenanthrene-1-carboxylic acid (1)
1-(9Z-Octadecenoyl)-sn-glycero-3-phosphocholine (1)
1-Heptadecanoyl-sn-glycero-3-phosphocholine (1)
1-Hexadecanoyl-sn-glycerol (1)
1-Hexadecyl-sn-glycero-3-phosphocholine (1)
1-Myristoyl-2-stearoyl-sn-glycero-3-phosphocholine (1)
1-Myristoyl-sn-glycero-3-phosphocholine (1)
1-Palmitoyl-2-myristoyl-sn-glycero-3-phosphocholine (1)

IsPrivate

False (1)

Modelling Approach

Ordinary differential equation model (1)

Study type

Transcription profiling by array (14)
RNA-seq of coding RNA (7)
Unknown experiment type (2)
RIP-seq (2)
Transcription profiling by SAGE (1)
Comparative genomic hybridization by array (1)
DNA-seq (1)
Methylation profiling by array (1)
RNA-seq of coding RNA from single cells (1)
RNA-seq of non coding RNA (1)

Release Date

2021 (121)
2023 (117)
2022 (107)
2025 (106)
2020 (87)
2024 (87)
2019 (77)
2018 (61)
2015 (54)
2017 (45)
2016 (37)
2013 (37)
2014 (35)
2011 (31)
2012 (26)
2026 (19)
2010 (15)
2009 (14)
2006 (8)
2008 (7)
2007 (7)
2005 (2)
2004 (2)
2003 (2)
2002 (1)

Lab affiliation

The University of Melbourne (4)
Applied Bioinformatics of Cancer University of Edinburgh Cancer Research Centre Institute of Genetics and Molecular Medicine Edinburgh, United Kingdom (1)
Center for Translational & Computational Neuroimmunology Department of Neurology 622 West 168th street New York, NY 10032 (1)
Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK (1)
Cornell University (1)
Department of Biological Engineering, MIT (1)
Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas (1)
Dynamic Omics, Antibody Discovery and Protein Engineering (ADPE), R&D AstraZenecaGaithersburg, Maryland, US, 20878. (1)
Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V. Otto-Hahn-Straße 6b 44227 Dortmund, Germany P: +49 (0)2 31.13 92-100 F: +49 (0)2 31.13 92-200 www.isas.de (1)
Molecular Allergy Research Laboratory, Centre for Sustainable Tropical Fisheries and Aquaculture (CSTFA), College of Science and Engineering, James Cook University, Douglas, QLD 4811, Australia Tropical Futures Institute, James Cook University, 149 Sims Drive, Singapore 387380, Singapore (1)
Stoller Biomarker Discovery Centre, University of Manchester, United kingdom (1)
SynthSys University of Edinburgh (1)
The Institute of Cancer Research, London (1)
The Univeristy of Melbourne (1)
University of Oxford, Discovery Proteomics Facility, Target Discovery Institute (1)

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Effects of meteorological and land surface modeling uncertainty on errors in winegrape ET calculated with SIMS.

Not available

S-EPMC9509309 | biostudies-literature

Molecular changes during extended endocrine treatment of breast cancer

Sequential patient-matched samples treated with extended neoadjuvant therapy were studied. Samples were classified as pre-treatment (timepoint1, <0 days), early-on treatment (timepoint2, 0-120 days) and long-term treatment (timepoint4, >120 days).

ORGANISM(S): Homo sapiens (Human)

2019-02-27 | PXD009328 | Pride

Transcription profiling of brain from mice with multiple sclerosis, Alzheimers disease and permanent mid-cerebral artery occlusion from stroke to compare of gene expression changes characterizing these three different central nervous system pathologies

Three mouse models of human central nervous system pathologies were selected for analyzing gene expression changes compared to wild type normal brain. The selected models are: TgAPP23 for Alzheimerï¾’s disease (see Sturchler-Pierrat, C., Abramowski, D., Duke, M., Wiederhold, K.H., Mistl, C., Rothac...

ORGANISM(S): Mus musculus

2008-07-12 | E-MTAB-1 | biostudies-arrayexpress

In Situ Characterization of Hydrated Proteins in Water by SALVI and ToF-SIMS.

Not available

S-EPMC4828166 | biostudies-literature

ToF-SIMS evaluation of PEG-related mass peaks and applications in PEG detection in cosmetic products.

Not available

S-EPMC11217440 | biostudies-literature

Unraveling Neuronal Identities Using SIMS: A Deep Learning Label Transfer Tool for Single-Cell RNA Sequencing Analysis.

Not available

S-EPMC10002667 | biostudies-literature

Divergent Compensatory Responses to High Fat Diet Between C57BL6/J and C57BLKs/J Inbred Mouse Strains

To assess whether changes in islet gene expression contribute to differences in phenotypes in response to high fat diet or tretament with pioglitazone, Agilent Whole Mouse Genome Oligo Microarrays were performed on RNA isolated from islets of 4 mice per each treatment group for discovery analysis of...

ORGANISM(S): Mus musculus

2013-09-21 | E-GEOD-51055 | biostudies-arrayexpress

Chemical Evaluation of Eumelanin Maturation by ToF-SIMS and Alkaline Peroxide Oxidation HPLC Analysis.

Not available

S-EPMC7796430 | biostudies-literature

Dietary polyphenols promote resilience against sleep deprivation-induced cognitive impairment by activating protein translation.

Not available

S-EPMC6133707 | biostudies-literature

An unsupervised MVA method to compare specific regions in human breast tumor tissue samples using ToF-SIMS.

Not available

S-EPMC4783233 | biostudies-literature

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