Scott S A SA - OmicsDI

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Unknown (1050)
Transcriptomics (41)
Proteomics (31)
Genomics (6)
Metabolomics (3)
Multiomics (2)
Models (1)
Genomic (1)
Other (1)

Organisms

Homo sapiens (26)
Mus musculus (18)
Staphylococcus aureus (2)
Drosophila melanogaster (2)
Cryptosporidium parvum Iowa II (2)
Plasmodium yoelii yoelii 17XNL (1)
Oncorhynchus nerka (1)
Drosophila yakuba (1)
Aspergillus niger (1)
Arabidopsis lyrata (1)
Gasterosteus aculeatus (1)
Saccharomyces cerevisiae (1)
Escherichia coli str. K-12 substr. MG1655 (1)
Arabidopsis thaliana (1)
Danio rerio (1)
219334 (1)
Clathria prolifera (1)
Cryptosporidium parvum Iowa (1)
Lactobacillus acidophilus NCFM (1)
Limosilactobacillus reuteri subsp. reuteri (1)
Microcaldota (1)
Schizosaccharomyces pombe (1)

Repository

biostudies-arrayexpress (45)
pride (18)
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Tissue

Melanocyte (2)
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Kidney proximal convoluted tubule epithelial cell (1)
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Pancreas (1)
Pancreatic adenocarcinoma cell line (1)
Pancreatic islet beta cell (1)
Pancreatic islet cell (1)
Primary cell (1)

Disease

Melanoma (2)
Type 2 diabetes mellitus (2)
XCGD (1)
Not Available (1)
Breast cancer (1)
Developmental and epileptic encephalopathy 9 (1)
Disease free (1)
Lymphoma (1)
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Technology Type

Mass Spectrometry (18)
Shotgun proteomics (8)
Bottom-up proteomics (4)
Data-dependent acquisition (3)
Mass spectrometry (2)
Affinity purification coupled with mass spectrometry proteomics (2)
Top-down proteomics (2)
Data-independent acquisition (1)
SWATH MS (1)

Instrument Platform

Orbitrap Fusion Lumos (2)
Q Exactive (2)
Thermo Scientific Velos Pro mass spectrometer modified to enable 351 nm UVPD (2)
10X Genomics Chromium (1)
G2565BA DNA Scanner (1)
Illumina NovaSeq 6000 (1)
6545 Q-TOF LC/MS (1)
Instrument (1)
Orbitrap Eclipse (1)
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6230 TOF LC/MS (Agilent) (1)
Liquid Chromatography MS - positive - direct infusion (1)
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Applied biosystems / mds sciex qstar (1)
Thermo lcq deca (1)
Thermo lcq deca xp (1)
Thermo ltq (1)
UNKNOWN UNKNOWN (1)
Waters q-tof (1)

Publication Date

2013 (8)
2012 (8)
2023 (8)
2016 (7)
2011 (7)
2010 (6)
2024 (4)
2014 (4)
2025 (4)
2008 (3)
2007 (3)
2019 (3)
2021 (2)
2009 (2)
2020 (2)
2018 (2)
2017 (2)
2026 (2)
2005 (1)
2003 (1)
2015 (1)

CHEBI ID

CHEBI:10072 (1)
CHEBI:1015 (1)
CHEBI:1148 (1)
CHEBI:131434 (1)
CHEBI:133083 (1)
CHEBI:136236 (1)
CHEBI:136239 (1)
CHEBI:136245 (1)
CHEBI:138364 (1)
CHEBI:138367 (1)
CHEBI:138368 (1)
CHEBI:140361 (1)
CHEBI:140362 (1)
CHEBI:14314 (1)
CHEBI:14336 (1)
CHEBI:15344 (1)
CHEBI:15346 (1)
CHEBI:15351 (1)
CHEBI:15354 (1)
CHEBI:15422 (1)
CHEBI:15428 (1)
CHEBI:15584 (1)
CHEBI:15611 (1)
CHEBI:15647 (1)
CHEBI:15674 (1)
CHEBI:15676 (1)
CHEBI:15682 (1)
CHEBI:15698 (1)
CHEBI:15700 (1)
CHEBI:15724 (1)

Metabolite Name

1,2-Dipalmitin (1)
1-Aminocyclopropanecarboxylic Acid (1)
1-Hydroxy-2-naphthoic Acid (1)
1-Pyrroline-2-carboxylic acid (1)
12-Hydroxydodecanoic Acid (1)
2'-Deoxyguanosine (1)
2'-Deoxyguanosine 5'-Diphosphate (dGDP) (1)
2,4-Dihydroxypteridine (Lumazine) (1)
2,6-Dihydroxypyridine (1)
2-Aminoadipic Acid (1)
2-Aminoisobutyric acid (1)
2-Hydroxy-3-methylpentanoic acid (1)
2-Hydroxybutyric acid (1)
2-Ketobutyric Acid (1)
2-Oxoadipic Acid (1)
2-Oxoglutaric Acid (1)
2-Phosphoglyceric acid (1)
2-Pyridinylacetic acid (1)
2-hydroxyisobutyric acid (1)
3,4-Dihydroxymandelic Acid (1)
3-Amino-4-Hydroxybenzoic Acid (3,4-AHBA) (1)
3-Amino-5-Hydroxybenzoic Acid (AHBA) (1)
3-Aminoisobutyric acid (1)
3-Hydroxyanthranilic Acid (1)
3-Hydroxybutyric acid (1)
3-Hydroxyglutaric Acid (1)
3-Hydroxymethylglutaric Acid (1)
3-Hydroxyphenylacetic Acid (1)
3-Phospho-D-glycerate (1)
3-Phosphoglyceroinositol (1)

IsPrivate

False (1)

Model Flag

Non Kinetic (1)

Submitter Keywords

FROG (1)

Modelling Approach

Constraint-based model (1)

Modification

Not available (1)

Study type

Transcription profiling by array (26)
RNA-seq of coding RNA (5)
ChIP-seq (4)
Unknown experiment type (3)
Other (2)
ChIP-chip by tiling array (1)
Transcription profiling by RT-PCR (1)
Comparative genomic hybridization by array (1)
RNA-seq of coding RNA from single cells (1)
RNA-seq of non coding RNA (1)

Release Date

2021 (120)
2022 (116)
2023 (104)
2020 (90)
2025 (89)
2024 (88)
2019 (65)
2017 (60)
2018 (59)
2015 (52)
2016 (42)
2013 (42)
2012 (35)
2014 (34)
2011 (28)
2010 (22)
2026 (13)
2009 (12)
2008 (11)
2006 (5)
2004 (3)
2007 (2)
2005 (2)
2003 (1)

Lab affiliation

Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia. (3)
Department of Chemistry and Biochemistry University of Colorado, Boulder Boulder, CO 80309 (2)
Associate Professor Department of Biological Sciences University of Denver (1)
Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington DC, USA (1)
Children's Hospital of Philadelphia 416B Abramson Pediatric Research Center Philadelphia, PA 19104 Office: 215-590-5320 Lab: 215-590-5319 (1)
Department of Biochemistry & Pharmacology, Bio21 Molecular Science and Biotechnology Institute The University of Melbourne, Victoria, 3010 Australia (1)
Department of Nutrition and Integrative Physiology, College of Health, University of Utah, UT 84112, USA Diabetes and Metabolism Research Center, University of Utah, UT 84112, USA (1)
Department of Pharmacology and Lineberger Comprehensive Cancer Center at University of North Carolina at Chapel Hill (1)
Departments of Genetics and Biochemistry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA (1)
Division of Metabolism, Endocriology & Diabetes and Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, USA (1)
Division of Metabolism, Endocriology & Diabetes and Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, USA. (1)
GlaxoSmithKline (GSK) (1)
MIT (1)
Sequence database group (1)
University of Melbourne, Melbourne, Australia (1)

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Coronary Plaque Burden in South Asian Adults: Insights From the DILWALE Registry.

Not available

S-EPMC13627118 | biostudies-literature

Pharmacognostic Evaluation, Chemical Characterization, and Antibacterial Activity of Bassia indica (Wight) A.J. Scott.

Not available

S-EPMC11244141 | biostudies-literature

S-Nitrosylation-mediated dysfunction of TCA cycle enzymes in synucleinopathy studied in postmortem human brains and hiPSC-derived neurons

A causal relationship between mitochondrial metabolic dysfunction and neurodegeneration has been strongly implicated in synucleinopathies, including Parkinson’s disease (PD) and Lewy body dementia (LBD), but the underlying molecular basis is not fully understood. Here, using human induced pluripoten...

ORGANISM(S): Homo sapiens (Human)

2024-10-17 | PXD036797 | Pride

Becker2005 - Genome-scale metabolic network of Staphylococcus aureus (iSB619)

Becker2005 - Genome-scale metabolic network of Staphylococcus aureus (iSB619) This model is described in the article: Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. Becker SA, Palsson BØ. ...

2024-10-15 | MODEL1507180070 | BioModels

FROG

NPC1 regulates the distribution of phosphatidylinositol 4 kinases at Golgi and Lysosome membranes

Cholesterol and phosphoinositides (PI) are two critically important lipids that are found in cellular membranes and dysregulated in many disorders. Therefore, uncovering molecular pathways connecting these essential lipids may offer new therapeutic insights. We report that loss of function of lysoso...

2021-09-15 | MTBLS2612 | MetaboLights

RNA-seq reveals differential gene expression in Staphylococcus aureus at single-nucleotide resolution

Staphylococcus aureus is a gram-positive cocci and an important human commensal bacteria and pathogen. S. aureus infections are increasingly difficult to treat because of the emergence of highly resistant MRSA (Methicillin-resistant S. aureus) strains. Here we present a method to study differential...

ORGANISM(S): Staphylococcus aureus

2013-11-07 | E-GEOD-48896 | biostudies-arrayexpress

Aurora B opposes PP1 function in mitosis through phosphorylation of the conserved RVxF binding motif in PP1 regulatory proteins

Protein phosphatase 1 (PP1) is a highly conserved protein phosphatase that opposes the actions of a diverse set of Ser-Thr protein kinases by controlling the majority of serine-threonine (Ser-Thr) dephosphorylation reactions in eukaryotes. PP1 gains substrate specificity through binding to a large n...

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

2018-03-30 | MSV000082226 | MassIVE

Gene expression profiles of murine granule neuron precursors and medulloblastoma

Sonic hedgehog (Shh) signals via Gli transcription factors to stimulate proliferation of granule neuron precursor cells (GNPs) in the cerebellum. Deregulation of Shh target genes often results in unrestrained GNP proliferation and eventually medulloblastoma (MB), the most common pediatric brain mali...

ORGANISM(S): Mus musculus

2010-06-16 | E-GEOD-17702 | biostudies-arrayexpress

Quantitative phosphoproteomics reveals pathways for coordination of cell growth and division by the fission yeast DYRK kinase Pom1

Data from ProteomeXchange, PXD ID:PXD001649 . File: o53292.mzml. Published as part of Mol Cell Proteomics. 2015 Feb 26 . From the Abstract: {{i}} ... Here, we sought to determine the phosphorylation targets of Pom1 kinase activity by SILAC-based phosphoproteomics. We defined a set of high-confidenc...

ORGANISM(S): S_pombe

GPM32320013881 | GPMDB

Resource Reanalysis

Transcription Response by sulfur chemolithoautotroph Thiomicrospira crunogenato dissolved inorganic carbon and ammonia limitation

The hydrothermal vent gammaproteobacterium Thiomicrospira crunogena inhabits an unstable environment and must endure dramatic sweeps in habitat chemistry. This sulfur chemolithoautotroph responds to changes in dissolved inorganic carbon (DIC; = CO2 + HCO3- + CO3-2) availability with a carbon concent...

ORGANISM(S): Thiomicrospira crunogena

2012-03-04 | E-GEOD-36254 | biostudies-arrayexpress

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