Murphy D D - OmicsDI

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Unknown (4248)
Transcriptomics (186)
Proteomics (82)
Genomics (67)
Metabolomics (31)

Organisms

Homo sapiens (107)
Mus musculus (85)
Bombyx mori (76)
Schizosaccharomyces pombe (76)
Human immunodeficiency virus 1 (76)
Oryza sativa Indica Group (76)
Sinorhizobium meliloti BL225C (76)
Sus scrofa domesticus (76)
Ostreococcus tauri (76)
Saccharomyces cerevisiae (76)
Vitis vinifera (76)
Rattus norvegicus (9)
Caenorhabditis elegans (8)
Drosophila melanogaster (3)
Macaca mulatta (2)
Bos taurus (2)
Danio rerio (2)
Cryptomys hottentotus hottentotus (1)
Pan troglodytes (1)
Equus caballus (1)
Zea mays (1)
Geobacter sulfurreducens (1)
Staphylococcus aureus (1)
Apis mellifera mellifera (1)
Solanum tuberosum (1)
Escherichia coli (1)
Saccharomyces cerevisiae (1)
Sus scrofa (1)
Arabidopsis thaliana (1)
Glycocystis (1)

Organisms

Dibamus cf. smithi (3)
Gastrophryne carolinensis (3)
Rhineura floridana (3)
Macrochelys suwanniensis (3)
Manis pentadactyla (3)
Homo sapiens (1)

Repository

biostudies-arrayexpress (199)
pride (76)
EGA (30)
MetaboLights (29)
ENA (23)
MassIVE (5)
GNPS (2)
geo (1)
PAXDB (1)

Tissue

Cell culture (10)
Brain (7)
Whole body (5)
Fibroblast (5)
Epithelial cell (5)
Prostate adenocarcinoma cell line (3)
Epithelial cell of prostate (3)
Permanent cell line cell (3)
T cell (3)
Skin (2)
Macrophage (2)
Heart (2)
Skeletal muscle (2)
Cell suspension culture (2)
Blood plasma (2)
Spleen (2)
Neutrophil (2)
Colon (2)
Blood (2)
Neurohypophysis (1)
Raphe nuclei (1)
Pancreatic cancer cell (1)
Myotube (1)
Plasma cell (1)
T-lymphocyte cell line (1)
Aorta (1)
Natural killer cell (1)
Venom (1)
Pancreas (1)
Brown adipose tissue (1)

Disease

Prostate carcinoma (3)
Neuroblastoma (2)
Multiple myeloma (2)
Myocardial ischemia (2)
Colon cancer (2)
HPV positive (1)
Pancreatic tumor (1)
Melanoma (1)
Osteosarcoma (1)
Normal (1)
Asbestos-related lung carcinoma (1)
Low birth weight (1)
Fibrolamellar carcinoma (1)
Neurological dysfunction (1)
Avian influenza (1)
Mental depression (1)
Lymphoma (1)
Pancreatic ductal adenocarcinoma (1)
Adult respiratory distress syndrome (1)
Cardiovascular system disease (1)
Parkinson's disease (1)
Type 2 diabetes mellitus (1)

Technology Type

Mass Spectrometry (76)
Shotgun proteomics (40)
Mass spectrometry (28)
Bottom-up proteomics (16)
Data-dependent acquisition (10)
Affinity purification coupled with mass spectrometry proteomics (8)
SWATH MS (5)
Gel-based experiment (4)
Data-independent acquisition (3)
Top-down proteomics (3)
SRM/MRM (2)
ILLUMINA, Illumina HiSeq 4000, Illumina HiSeq 2500 (1)
Affymetrix OncoScan FFPE Express (1)
Illumina HiSeq 2500, ILLUMINA, Illumina MiSeq (1)
Illumina MiSeq (1)
Mass spectrometry assay (1)

Instrument Platform

Liquid Chromatography MS - positive - reverse phase (15)
NextSeq 500 (12)
Liquid Chromatography MS - negative - reverse phase (10)
Illumina HiSeq 2000 (4)
Direct infusion MS - negative (3)
Direct infusion MS - positive (3)
Liquid Chromatography MS - negative - hilic (3)
Illumina Genome Analyzer IIx (2)
Illumina Genome Analyzer II (2)
Illumina NovaSeq 6000 (2)
DNBSEQ-G400 FAST (1)
DNA Microarray Scanner (Model G2505C, Agilent Technologies) (1)
N/A (1)
NextSeq 550 (1)
Illumina HiSeq 2500 (1)
Illumina HiSeq 4000 (1)
MicrOTOF-Q II (1)
MaXis (1)
LTQ FT (1)
LTQ (1)
Orbitrap Exploris 480 (1)
Q Exactive HF-X (1)
Orbitrap Fusion Lumos (1)
Q Exactive HF (1)
Liquid Chromatography MS -neg - hilic (1)
Liquid Chromatography MS – pos - hilic (1)
LTQ XL (Thermo Scientific) (1)
LTQ Orbitrap XL (Thermo Scientific) (1)
Liquid Chromatography MS - Positive (LC-MS (Positive)) (1)
Direct infusion MS - (1)

Publication Date

2015 (29)
2010 (29)
2023 (26)
2008 (25)
2014 (19)
2024 (17)
2012 (16)
2011 (16)
2016 (15)
2021 (14)
2018 (14)
2013 (14)
2020 (13)
2022 (12)
2026 (11)
2025 (11)
2009 (10)
2007 (7)
2019 (6)
2005 (3)
2003 (3)
2006 (2)
2017 (1)

UNIPROT ID/AC

Q88R08_PSEPK (1)
PURA_PSEPK (1)
ILVC_PSEPK (1)
Q88DD0_PSEPK (1)
Q88CH2_PSEPK (1)
Q88FF0_PSEPK (1)
Q88IX4_PSEPK (1)
Q88QE5_PSEPK (1)
RSGA_PSEPK (1)
MURC_PSEPK (1)
HIS3_PSEPK (1)
Q88PI6_PSEPK (1)
Q88C77_PSEPK (1)
Q88FZ6_PSEPK (1)
Q88ET5_PSEPK (1)
Q88NX2_PSEPK (1)
Q88RK6_PSEPK (1)
Q88KZ4_PSEPK (1)
Q88CH1_PSEPK (1)
Q88QE4_PSEPK (1)
Q88NX1_PSEPK (1)
Q88C76_PSEPK (1)
MOBA_PSEPK (1)
Q88PS9_PSEPK (1)
GCSH1_PSEPK (1)
ILVD_PSEPK (1)
Q88R07_PSEPK (1)
Q88DX6_PSEPK (1)
Q88E96_PSEPK (1)
Q88IX3_PSEPK (1)

CHEBI ID

CHEBI:16196 (5)
CHEBI:17351 (5)
CHEBI:30769 (5)
CHEBI:85700 (4)
CHEBI:16359 (4)
CHEBI:30915 (4)
CHEBI:35038 (3)
CHEBI:134435 (3)
CHEBI:85698 (3)
CHEBI:72998 (3)
CHEBI:28842 (3)
CHEBI:64563 (3)
CHEBI:28716 (3)
CHEBI:15603 (3)
CHEBI:28865 (3)
CHEBI:16865 (3)
CHEBI:18012 (3)
CHEBI:73024 (3)
CHEBI:16856 (3)
CHEBI:17858 (3)
CHEBI:15741 (3)
CHEBI:6650 (3)
CHEBI:16919 (3)
CHEBI:18257 (3)
CHEBI:18237 (3)
CHEBI:25017 (3)
CHEBI:29016 (3)
CHEBI:138900 (2)
CHEBI:88466 (2)
CHEBI:182784 (2)

Metabolite Name

Cholic acid (4)
Tris(2-butoxyethyl) phosphate (3)
PC(16:0/0:0) (3)
9(10)-EpOME (3)
Linoleic acid (3)
1,20-Eicosanediol (2)
Dibutyl phthalate (DBP) (2)
Lyso-PC(16:0) (2)
Alpha-linolenic acid|linolenic acid|(9Z,12Z,15Z)-octadeca-9,12,15-trienoic 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)
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)
(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)
PC(18:2/18:2) (2)
Glutathione disulfide (2)
Phosphatidylcholine 40:1 (2)
Phosphatidylcholine 34:1 (2)
Phosphatidylcholine 32:1 (2)
Phosphatidylethanolamine 38:1 (2)
Phosphatidylethanolamine 36:0 (2)
Phosphatidylcholine 38:2 (2)
Phosphatidylcholine 37:3 (2)
Diacylglycerol 36:3 (2)
Glutathione (2)
2,6-Di-tert-butyl-4-hydroxymethylphenol (2)
Phloretin (2)
Levulinic acid (2)
Undecylenic acid (2)
Myristoleic acid (2)
Taurocholic acid (2)
1-Stearoyl-2-hydroxy-sn-glycero-3-phosphocholine (2)

First Public Date

2023 (12)
2024 (6)
2022 (2)
2026 (1)
2025 (1)
2015 (1)

Modification

Not available (1)

Study type

Transcription profiling by array (136)
RNA-seq of coding RNA (24)
ChIP-seq (13)
RNA-seq of coding RNA from single cells (5)
Unknown experiment type (3)
Methylation profiling by array (3)
RNA-seq of non coding RNA (3)
RNAi profiling by array (2)
Comparative genomic hybridization by array (2)
One-color microarray (1)
Human - High-throughput sequencing (1)
Animal - High-throughput sequencing (1)
Cell line - High-throughput sequencing (1)
ChIP-chip by array (1)
Other (1)
ScATAC-seq (1)
Methylation profiling by high throughput sequencing (1)

Release Date

2022 (501)
2021 (444)
2023 (420)
2025 (361)
2024 (340)
2020 (340)
2018 (292)
2019 (246)
2015 (218)
2017 (211)
2016 (191)
2014 (162)
2013 (133)
2011 (115)
2012 (110)
2010 (100)
2008 (68)
2009 (54)
2026 (42)
2007 (19)
2006 (19)
2005 (14)
2003 (12)
2004 (10)
2001 (8)
2000 (7)
2002 (5)
1998 (2)
1997 (2)
1999 (1)

Lab affiliation

Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, W12 0BZ, UK The Francis Crick Institute, London, NW1 1AT, UK (4)
CRUK - Beatson Institute for Cancer Research - Switchback Rd, Bearsden, Glasgow G61 1BD - United Kingdom (3)
Department of Pathology, Dalhousie University (2)
The University of Melbourne (2)
IUSM Center for Proteome Analysis, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN (1)
James McGill Professor of Neurology and Neurosurgery and Anatomy and Cell Biology Montreal Neurological Institute-Hospital McGill, Montreal CANADA (1)
Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland (1)
Department of Chemistry, Imperial College London, Molecular Research Science Hub, 80 Wood Lane, London W12 0BZ, United Kingdom. The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom. (1)
NDM Research Building | Old Road Campus | Oxford OX3 7FZ (1)
Children's Medical Research Institute, Faculty of Medicine and Health, Westmead, NSW, Australia (1)
Department of Biochemistry, Monash University, Clayton,3168, Australia (1)
Faculty Scientist Maine Medical Center Research Institute Scarborough, Maine United States (1)
1. Garvan Institute of Medical Research, Cancer Ecosystems Program, and The Kinghorn Cancer Centre, Darlinghurst, Sydney, New South Wales, Australia. 2. School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales (UNSW), Kensington, Sydney, New South Wales, Australia. (1)
Head, Inflammation Division Professor and NHMRC Leadership Fellow Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville, VIC 3052, Australia (lab head) (1)
School of Physiology, Pharmacology and Neuroscience University of Bristol Biomedical Sciences Building University Walk Bristol - BS8 1TDE United Kingdom (1)
Head, Inflammation Division Professor and NHMRC Leadership Fellow Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville, VIC 3052, Australia (1)
Faculty of Human and Medical Science (1)
Department of Biochemistry, University of Washington, Seattle, WA, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA Institute for Protein Design, University of Washington, Seattle, WA, USA (1)
The Centre for Cancer Biology (1)
Baker Heart and Diabetes Institute, Aus (1)
Molecular Neuroendocrinology Group, Translational Health Sciences, Bristol Medical School, University of Bristol (1)
The Institute of Cancer Reaserach Moecular and Systems Oncology (1)
Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3052 Australia (1)
Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom (1)
MPI of Biophysics and Brain Research (1)
Department of Biochemistry and Microbiology, L-Probe Lab Ghent University (1)
6Department of Molecular Science/UT Health Rio Grande Valley, USA (1)
Maynooth University Department of Biology Maynooth University, Maynooth, Co. Kildare, Ireland. (1)
Molecular Neuroendocrinology group, Bristol Medical school, University of Bristol (1)
Dept of Chemistry, University of Illinois at Urbana-Champaign (1)

Tags

xref:PubMed:33911273 (8)

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Metabolomics to elucidate the effects of novel sustainable feed additives in the feed of farmed salmon (HoloFood Trial D - fermented seaweed open water-dose response)

Testing the effect of seaweed as a novel cost-efficient feed source for Atlantic salmon feed. Fermentation of novel raw materials for fish feed is a new practice with little prior experience of direct relevance to aquaculture and fish farming. In Trial D, an alternative marine compound is include...

2023-06-13 | MTBLS6733 | MetaboLights

Analysis of Ppif-/- hearts

To identify differences in gene expression between peptidylprolyl isomerase F (cyclophilin D; Ppif)-null hearts and WT control hearts. RNA was isolated from mice 8 weeks of age to discover gene changes prior to myocardial dysfunction. Three replicates each of Ppif-/- and WT mice.

ORGANISM(S): Mus musculus

2011-01-05 | E-GEOD-23028 | biostudies-arrayexpress

Transcription profiling of human Caco-2 cells treated with conjugated linoleic acid (CLA)

The effect of CLA on gene expression in Caco-2 cells Experiment Overall Design: Caco-2 cells were treated with linoleic acid (LA; the parent and control fatty acid) trans-10, cis-12 CLA or cis-9, trans-11 CLA for 12 d.

ORGANISM(S): Homo sapiens

2008-06-14 | E-GEOD-6518 | biostudies-arrayexpress

Gene expression profiling of mouse splenic Dendritic cells subsets

We describe a novel subset of CD8+ DCs in lymphoid organs of naïve mice characterized by expression of the CX3CR1 chemokine receptor. CX3CR1+CD8+ DCs lack hallmarks of classical CD8+ DCs, including IL12 secretion, the capacity to cross-present antigen and their developmental independence of the tran...

ORGANISM(S): Mus musculus

2010-07-28 | E-GEOD-23212 | biostudies-arrayexpress

Effect of Monthly High-Dose Vitamin D Supplementation on Cardiovascular Disease in the Vitamin D Assessment Study : A Randomized Clinical Trial.

Not available

S-EPMC5815022 | biostudies-literature

Combined Neuropeptide S and D-Cycloserine Augmentation Prevents the Return of Fear in Extinction-Impaired Rodents: Advantage of Dual versus Single Drug Approaches.

Not available

S-EPMC4926792 | biostudies-literature

Factors associated with D-dimer levels in HIV-infected individuals.

Not available

S-EPMC3953205 | biostudies-literature

Expression data from C57BL/6J and MRL/MpJ hearts following acute myocardial infarction

The Murphy Roth Large (MRL) mouse, a strain capable of regenerating right ventricular myocardium, has a high post-myocardial infarction (MI) survival rate compared with C57BL6/J (C57) mice. The biological processes responsible for this survival advantage are unknown. We compared acute post-MI gene e...

ORGANISM(S): Mus musculus

2010-05-27 | E-GEOD-19322 | biostudies-arrayexpress

Not available

S-EPMC6722852 | biostudies-literature

Elements between the IgH variable (V) and diversity (D) clusters influence antisense transcription and lineage-specific V(D)J recombination.

Not available

S-EPMC3009784 | biostudies-literature

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4614 Results

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