Wood R E RE - OmicsDI

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Unknown (300)
Genomics (29)
Transcriptomics (28)
Metabolomics (11)
Proteomics (9)

Organisms

Homo sapiens (38)
Mus musculus (8)
Gallus gallus (4)
Danio rerio (2)
Rhodospirillum rubrum (1)
Populus x canadensis (1)
Candida dubliniensis (1)
Schizosaccharomyces pombe (1)
Trypanosoma brucei (1)
Mycobacterium tuberculosis (1)
Populus tremula x Populus alba (1)
Pseudomonas aeruginosa UCBPP-PA14 (1)
Escherichia coli (1)
Rattus norvegicus (1)
Aquifex aeolicus (1)
Clostridium autoethanogenum (1)

Repository

biostudies-arrayexpress (30)
EGA (28)
MetaboLights (11)
pride (6)
MassIVE (1)
PeptideAtlas (1)

Tissue

Cell culture (2)
Cell suspension culture (1)
Hepatocyte (1)
Macrophage (1)
Muscle (1)
Muscle cell (1)
Neuron (1)
Pluripotent stem cell (1)
Prokaryotic cell (1)
T cell (1)

Disease

Hereditary spastic paraplegia 47 (1)
Hereditary spastic paraplegia 50 (1)
Hereditary spastic paraplegia 51 (1)
Hereditary spastic paraplegia 52 (1)
Neuroblastoma (1)

Technology Type

Mass spectrometry (9)
Mass Spectrometry (6)
Bottom-up proteomics (3)
Mass spectrometry assay (2)
Shotgun proteomics (2)
AB SOLiD 4 System, Illumina HiSeq 2500, Illumina HiSeq 2000, AB SOLiD System 3.0 (1)
Data-dependent acquisition (1)
SWATH MS (1)

Instrument Platform

Liquid Chromatography MS - negative - hilic (4)
Liquid Chromatography MS - positive - reverse phase (3)
DNA Microarray Scanner BA [Agilent Technologies] (2)
LTQ Orbitrap Velos (2)
Liquid Chromatography MS - negative - reverse phase (2)
Liquid Chromatography MS - positive - hilic (2)
HiSeq X Ten (1)
Illumina HiSeq 2500 (1)
Illumina NovaSeq 6000 (1)
5975C Series GC/MSD (Agilent) (1)
6530 Q-TOF LC/MS (Agilent) (1)
Gas Chromatography MS - positive (1)
Liquid Chromatography MS - (1)
Liquid Chromatography MS - alternating - reverse phase - Exactive (Thermo Scientific) (1)
Q Exactive (1)
SYNAPT HDMS (Waters) (1)

Publication Date

2010 (6)
2024 (4)
2021 (4)
2015 (4)
2009 (4)
2006 (4)
2014 (3)
2026 (3)
2025 (3)
2013 (2)
2011 (2)
2023 (2)
2020 (2)
2017 (2)
2018 (1)
2016 (1)
2012 (1)
2007 (1)

UNIPROT ID/AC

A0A5E1 (1)
A0ELI5 (1)
A0EQY3 (1)
A0JLQ7 (1)
A0JNY3 (1)
A0JNY7 (1)
A0MNP4 (1)
A0PJD7 (1)
A0PJL0 (1)
A0PK78 (1)
A0PK81 (1)
A1A553 (1)
A1A557 (1)
A1A558 (1)
A1A596 (1)
A1A5B6 (1)
A1E5T5 (1)
A1ILG8 (1)
A1L013 (1)
A1L0U3 (1)
A1L0U6 (1)
A1L0V6 (1)
A1L317 (1)
A1L329 (1)
A1L341 (1)
A1L347 (1)
A1L353 (1)
A1L361 (1)
A1L366 (1)
A1L3B6 (1)

ENSEMBL ID

ENSMUSG00000021039 (1)
ENSMUSG00000027651 (1)
ENSMUSG00000098557 (1)
ENSMUSP00000069525 (1)
ENSMUSP00000140201 (1)
ENSMUSP00000141097 (1)
ENSMUSP00000141637 (1)

CHEBI ID

CHEBI:16347 (3)
CHEBI:17750 (3)
CHEBI:16335 (2)
CHEBI:16708 (2)
CHEBI:17596 (2)
CHEBI:17924 (2)
CHEBI:18050 (2)
CHEBI:27432 (2)
CHEBI:78320 (2)
CHEBI:1230 (1)
CHEBI:132553 (1)
CHEBI:132673 (1)
CHEBI:132676 (1)
CHEBI:132957 (1)
CHEBI:133221 (1)
CHEBI:133244 (1)
CHEBI:133521 (1)
CHEBI:134270 (1)
CHEBI:134271 (1)
CHEBI:134428 (1)
CHEBI:134451 (1)
CHEBI:136186 (1)
CHEBI:136203 (1)
CHEBI:136236 (1)
CHEBI:136239 (1)
CHEBI:136243 (1)
CHEBI:136256 (1)
CHEBI:136259 (1)
CHEBI:136445 (1)
CHEBI:136579 (1)

Metabolite Name

D-Sorbitol (2)
(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 (1)
(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)
(S)-3-Hydroxytetradecanoyl-CoA (1)
1,2-bis-O-Sinapoyl-beta-D-glucoside (1)
1-(sn-Glycero-3-phospho)-1D-myo-inositol (1)
1-Isothiocyanato-6-(methylthio)hexane (1)
10-OPDA (1)
12,13-Epoxylinolenate (1)
12-OPDA/12-oxo-PDA (1)
13-Keto-9Z,11E-octadecadienoic acid (1)
2,4-Dihydroxylamino-6-nitrotoluene (1)
2,5-Dihydroxybenzoate 2-O-β-D-glucoside (1)
2,6-Di-tert-butyl-4-hydroxymethylphenol (1)
2-(3-benzoylphenyl)-3,5,7-trihydroxychromen-4-one (1)
2-Hydroxy-3-butenyl-desulfoglucosinolate (1)
2-Hydroxy-linoleic acid (1)
2-Oxindole-3-acetyl-β-D-glucose (1)
2-Oxo-6-methylthiohexanoate (1)
2-Oxo-9-methylthiononanoate (1)
2-aminooctanoic acid (1)
3-Hydroxy-L-proline (1)
3-Methoxysalicylic acid (1)
3-hydroxybutyric acid (1)
3-hydroxypentanoic acid (1)
3alpha,7alpha-dihydroxy-12-oxo-5beta-cholanic acid (1)
3beta-Hydroxy-5-cholenoic acid (1)
4'-Dihydroabscisic acid (1)
4-Fluorocatechol (1)

Study type

Transcription profiling by array (23)
RNA-seq of coding RNA (2)
ChIP-chip by tiling array (1)
Proteomic profiling by mass spectrometer (1)
ChIP-seq (1)
CUT&RUN (1)
Genotyping by high throughput sequencing (1)

Release Date

2021 (45)
2022 (40)
2020 (34)
2023 (29)
2024 (20)
2018 (20)
2025 (19)
2014 (14)
2015 (13)
2010 (13)
2019 (13)
2016 (11)
2013 (10)
2011 (10)
2012 (8)
2026 (8)
2017 (6)
2009 (5)
2006 (4)
2008 (4)
2007 (3)
2003 (1)

Lab affiliation

Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Australia (1)
Department of Neurology, School of Medicine, Yale University, New Haven (CT), USA (1)
Department of Physiology, University of Kentucky, USA (1)
Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany (1)
PhD student, Department of Biochemistry, Emory University (1)
Proteomic Platform of Institut de Microbiologie de la Méditerranée CNRS FR 3479 (1)

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Assessment of human plasma and urine sample preparation for re-producible and high-throughput UHPLC-MS clinical metabolic phenotyping

Clinical metabolic phenotyping employs metabolomics and lipidomics to detect and measure thousands of metabolites and lipids within human samples. This approach aims to identify metabolite and lipid changes between phenotypes (e.g. disease status) that aid understanding of biochemical mechanisms ...

2020-08-06 | MTBLS1465 | MetaboLights

Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees

Background

Bioconversion of wood into bioproducts and biofuels is hindered by the recalcitrance of woody raw material to bioprocesses such as enzymatic saccharification. Targeted modification of the chemical composition of the feedstock can improve saccharification but this gain is often abr...

2021-10-06 | MTBLS628 | MetaboLights

Transcription profiling of E. coli planktonic samples exposed to cis-1,2-dichloroethylene (cis-DCE)

Metabolically-engineered Escherichia coli has been used previously to degrade the ubiquitous pollutant cis-1,2-dichloroethylene (cis-DCE), and the impact of the metabolic engineering was assessed by investigating the changes in the proteome. Here, genome-wide transcriptome analysis was performed to...

ORGANISM(S): Escherichia coli

2009-11-27 | E-GEOD-13698 | biostudies-arrayexpress

Carbon fixation in the chemolithoautotrophic bacterium Aquifex aeolicus involves two low-potential ferredoxins as partners of the pentameric PFOR and OGOR enzymes

Aquifex aeolicus is a microaerophilic hydrogen- and sulfur -oxidizing bacterium that assimilates CO2 via the reverse tricarboxylic acid cycle (rTCA). Key enzymes of this pathway are pyruvate:ferredoxin oxidoreductase (PFOR) and 2-oxoglutarate:ferredoxin oxidoreductase (OGOR), which are responsible, ...

ORGANISM(S): Aquifex aeolicus

2023-05-10 | PXD040248 | Pride

Epicoccum layuense a potential biological control agent of esca-associated fungi in grapevine.

Not available

S-EPMC6435229 | biostudies-literature

Multiple oxygen tension environments reveal diverse patterns of transcriptional regulation in primary astrocytes

The central nervous system normally functions at O2 levels which would be regarded as hypoxic by most other tissues. However, most in vitro studies of neurons and astrocytes are conducted under hyperoxic conditions without consideration of O2-dependent cellular adaptation. We analyzed the reactivi...

ORGANISM(S): Rattus norvegicus

2012-09-20 | E-GEOD-29296 | biostudies-arrayexpress

The Populus transciptome in elevated CO2 reveals increased anthocyanin biosynthesis during delayed autumnal senescence

Over recent decades the progression of natural autumnal senescence has been increasingly delayed across wide areas of the Northern Hemisphere and is thought to be caused by rising temperature. Recently this delay has been shown to be partly attributable to rising atmospheric carbon dioxide concentr...

ORGANISM(S): Populus x canadensis

2010-01-31 | E-GEOD-15874 | biostudies-arrayexpress

Transcriptome of the maturing erythroblast

Understanding the pattern of gene expression and identifying the specific genes expressed during erythropoiesis is crucial for a synthesis of erythroid developmental biology. Here we have isolated four distinct populations of erythroblasts at successive erythropoietin-dependent stages of erythropoie...

ORGANISM(S): Homo sapiens

2011-03-02 | E-GEOD-22552 | biostudies-arrayexpress

RNA-seq of two human mammary epithelial cell lines (HMLE and HMLE-Twist-ER) treated with 4-hydroxytamoxifen vs control

Immortalized non-cancerous human mammary epithelial cells (HMLE) were transfected to express the murine fusion protein Twist1-estrogen receptor(point mutation G525R) (HTER). Twist1-mediated gene expression is activated by stimulation with 4-hydroxytamoxifen for several days and induces an epithelial...