Little David D - OmicsDI

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Unknown (283)
Transcriptomics (234)
Proteomics (50)
Genomics (30)
Metabolomics (4)
Genomic (2)
Multiomics (1)

Organisms

Homo sapiens (121)
Mus musculus (73)
Arabidopsis thaliana (13)
Rattus norvegicus (12)
Drosophila melanogaster (9)
Schizosaccharomyces pombe (6)
Saccharomyces cerevisiae (5)
Bos taurus (4)
Oryza sativa Japonica Group (2)
Escherichia coli (2)
Gallus gallus (2)
Acropora digitifera (1)
Influenza A virus (A/WSN/1933(H1N1)) (1)
Vibrio parahaemolyticus RIMD 2210633 (1)
Ampelisca abdita (1)
Acropora millepora (1)
Mustela putorius furo (1)
Influenza A virus (1)
Populus tremuloides (1)
Sarcophaga crassipalpis (1)
Pimephales promelas (1)
Leishmania donovani (1)
Prochlorococcus marinus (1)
Spodoptera frugiperda (1)
Gasterosteus aculeatus (1)
Ornithorhynchus anatinus (1)
unidentified (1)
Apis mellifera (1)
Zea mays (1)
Nasonia vitripennis (1)

Organisms

Drosophila serrata (1)
Arabidopsis thaliana (1)

Repository

biostudies-arrayexpress (254)
MassIVE (26)
pride (21)
EGA (10)
MetaboLights (3)
dbGaP (2)
jPOST (2)
ENA (2)
GNPS (1)

Tissue

Cell culture (5)
Brain (2)
Egg (2)
Embryo (2)
Embryonic stem cell (2)
Blood plasma (1)
Glial cell (1)
HEK-293T cell (1)
Heart (1)
Hippocampal neuron (1)
Kidney (1)
Mycelium (1)
NCI-H295R cell (1)
Placenta (1)
Primary cell (1)
Primary neuron (1)
Seminal plasma (1)
Sperm (1)
Spermatozoid (1)
Stem cell (1)
Whole body (1)

Disease

Scrapie infected (1)
Colon cancer metastasis (1)
Head and neck squamous cell carcinoma (1)
Glioblastoma (1)
Normal (1)
Breast cancer (1)
Disease free (1)

Technology Type

Mass Spectrometry (21)
Shotgun proteomics (13)
Bottom-up proteomics (6)
Mass spectrometry (3)
Affinity purification coupled with mass spectrometry proteomics (3)
Gel-based experiment (2)
ABI_SOLID, Illumina HiSeq 2000, Illumina 450K, AB 5500xl Genetic Analyzer, AB 5500 Genetic Analyzer, ILLUMINA (1)
ILLUMINA, Illumina HiSeq 2000 (1)
Illumina HiSeq 2000 (1)
Data-dependent acquisition (1)
Data-independent acquisition (1)
DiaPASEF (1)
HDMSE (1)

Instrument Platform

Q Exactive (8)
Illumina HiSeq 2500 (4)
Illumina Genome Analyzer IIx (3)
Illumina HiSeq 1000 (3)
Orbitrap Fusion (3)
Q Exactive HF-X (3)
Illumina HiSeq 2000 (2)
Illumina HiSeq 4000 (2)
Agilent 7890A GC system, Agilent 5975C MS detector (2)
LTQ Orbitrap (2)
NextSeq 2000 (1)
NextSeq 550 (1)
Illumina NovaSeq 6000 (1)
Exactive Plus (1)
LTQ (Thermo Scientific instrument model) (1)
LTQ Orbitrap Velos (1)
LTQ Orbitrap Velos ETD (1)
LTQ XL (1)
Q Exactive Plus (1)
Xevo G2-XS QTof (1)
6520 Q-TOF LC/MS (Agilent) (1)
Gas Chromatography MS - (1)
Liquid Chromatography MS - negative - reverse phase (1)
Liquid Chromatography MS - positive - reverse phase (1)

Publication Date

2013 (38)
2010 (34)
2015 (31)
2011 (30)
2014 (25)
2012 (25)
2016 (18)
2008 (15)
2009 (14)
2023 (11)
2017 (9)
2021 (8)
2018 (8)
2024 (6)
2007 (6)
2004 (5)
2022 (4)
2019 (4)
2026 (4)
2005 (3)
2006 (2)
2020 (2)
2025 (1)
2003 (1)

CHEBI ID

CHEBI:28044 (2)
CHEBI:131494 (1)
CHEBI:132244 (1)
CHEBI:133057 (1)
CHEBI:138389 (1)
CHEBI:139131 (1)
CHEBI:139133 (1)
CHEBI:139134 (1)
CHEBI:139136 (1)
CHEBI:139138 (1)
CHEBI:15356 (1)
CHEBI:15366 (1)
CHEBI:15428 (1)
CHEBI:15741 (1)
CHEBI:15756 (1)
CHEBI:15760 (1)
CHEBI:15882 (1)
CHEBI:15887 (1)
CHEBI:16135 (1)
CHEBI:16312 (1)
CHEBI:16325 (1)
CHEBI:16359 (1)
CHEBI:16390 (1)
CHEBI:16411 (1)
CHEBI:16449 (1)
CHEBI:16525 (1)
CHEBI:166731 (1)
CHEBI:166732 (1)
CHEBI:166734 (1)
CHEBI:16755 (1)

Metabolite Name

(-)-Epigallocatechin (1)
(.+/-.)-Lyoniresinol 2a-O-.beta.-D-glucopyranoside (1)
(.alpha.S,1S,2R)-.alpha.-Amino-2-carboxycyclopropaneacetic acid (1)
(1-Acetyloxy-3-hydroxy-6,8a-dimethyl-7-oxo-3-propan-2-yl-2,3a,4,8-tetrahydro-1H-azulen-4-yl) 4-hydroxybenzoate (1)
(1-Hydroxycyclohexyl)acetic acid (1)
(12Z)-9,10,11-Trihydroxyoctadec-12-enoic acid (1)
(17Z)-16-(Acetyloxy)-6-hydroxy-4,8,14-trimethyl-3,7-dioxo-18-norcholesta-17,24-dien-21-oic acid (1)
(2E)-N-(4-Acetamidobutyl)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enamide (1)
(2E,4E)-5-(6-((.beta.-D-Glucopyranosyloxy)methyl)-1-hydroxy-2,6-dimethyl-4-oxocyclohex-2-en-1-yl)-3-methylpenta-2,4-dienoic acid (1)
(2E,4E)-7,12-Dihydroxy-13-(hydroxymethyl)-3,5,7-trimethyltetradeca-2,4-dienedioic acid (1)
(2E,6E,10E,14S)-14-((2-O-.beta.-D-Glucopyranosyl-.beta.-D-glucopyranosyl)oxy)-2,6,10,14-tetramethylhexadeca-2,6,10,15-tetraenoic acid (1)
(2R,3R,4S,5S,6R)-2-Octoxy-6-[[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxymethyl]oxane-3,4,5-triol (1)
(2S)-2-[(2R,3S,7R,8R,8aS)-2,3,4'-Trihydroxy-4,4,7,8a-tetramethyl-6'-oxospiro[2,3,4a,5,6,7-hexahydro-1H-naphthalene-8,2'-3,8-dihydrofuro[2,3-e]isoindole]-7'-yl]-3-methylbutanoic acid (1)
(2S)-4-Amino-2-hydroxybutanoic acid (1)
(3-(Hexopyranosyloxy)-2-((2Z)-pent-2-en-1-yl)cyclopentyl)acetic acid (1)
(3.beta.,5.Xi.,8.alpha.,9.beta.,10.alpha.,16.beta.)-16-Hydroxykauran-3-yl .beta.-D-glucopyranoside (1)
(3.beta.,5.Xi.,9.Xi.,18.Xi.)-3,19-Dihydroxyurs-12-ene-24,28-dioic acid (1)
(3S,4S,6aR,6bS,8R,8aR,12aS,14bR)-8-Hydroxy-4,6a,6b,11,11,14b-hexamethyl-3-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicene-4,8a-dicarboxylic acid (1)
(3S,6R,12S)-6-Benzyl-3-butan-2-yl-9-(6,7-dihydroxyoctyl)-1,4,7,10-tetrazabicyclo[10.4.0]hexadecane-2,5,8,11-tetrone (1)
(4-(.beta.-D-Glucopyranosyloxy)-2,6-bis(3-methylbut-2-en-1-yl)phenyl)(hydroxy)acetic acid (1)
(5-Chloro-1H-benzimidazol-2-yl)methanol (1)
(5.Xi.,9.Xi.,18.Xi.)-3-Oxolup-20(29)-ene-27,28-dioic acid (1)
(7E)-11-Hydroxy-4,5,8,13,13-pentamethyl-3-(2-methylpropyl)-3,3a,4,6a,9,10,11,11a,14a,15-decahydro-1H-[1,3]dioxolo[9,10]oxacyclododecino[2,3-d]isoindole-1,16(2H)-dione (1)
(9Z,12E)-15,16-Dihydroxyoctadeca-9,12-dienoic acid (1)
(E)-1-Hydroxy-2-methylbut-2-enyl 4-diphosphate (1)
(E)-3,10-Dihydroxy-4,9-dimethyldodec-6-enedioic acid (1)
(E)-3-(4-Acetyloxy-2,3-dihydroxy-2,5,5,8a-tetramethyl-3,4,4a,6,7,8-hexahydro-1H-naphthalen-1-yl)prop-2-enoic acid (1)
(E)-4-Hydroxy-4-[4-hydroxy-2-[(E)-6-hydroxyhept-1-enyl]cyclopentyl]but-2-enoic acid (1)
(E)-4-[4-[(E)-Hept-1-enyl]-2,5-dihydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-6-yl]-2-methylbut-2-enoic acid (1)
(E)-5-Hydroxyundec-2-enoic acid (1)

First Public Date

2017 (1)
2014 (1)

Study type

Transcription profiling by array (146)
RNA-seq of coding RNA (43)
ChIP-seq (18)
Comparative genomic hybridization by array (9)
Other (7)
Methylation profiling by array (5)
ChIP-chip by tiling array (4)
Genotyping by array (4)
Unknown experiment type (3)
RNA-seq of non coding RNA (3)
Transcription profiling by SAGE (2)
ChIP-chip by array (2)
RNA-seq of coding RNA from single cells (2)
High-throughput sequencing (1)
Human - One-color microarray (1)
Transcription profiling by RT-PCR (1)
MicroRNA profiling by array (1)
Proteomic profiling by array (1)

Release Date

2015 (41)
2011 (38)
2013 (37)
2010 (37)
2023 (35)
2021 (35)
2012 (33)
2014 (31)
2016 (29)
2025 (28)
2018 (28)
2024 (27)
2022 (25)
2017 (19)
2009 (19)
2020 (19)
2019 (18)
2008 (15)
2007 (10)
2004 (5)
2006 (3)
2005 (3)
2003 (1)
2026 (1)

Lab affiliation

Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931 Cologne, Germany. (2)
Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic (2)
Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France (2)
1. Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 2. Division of Cardiology, Department od=f Pediatrics, University of Washington, Seattle, WA (1)
Babraham Institute (1)
Bioanalytical Research Labs, Department of Biology, University of Salzburg, Austria (1)
Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931 Cologne, Germany (1)
David Meierhofer, MS facility, Max Planck Institute for Molecular Genetics, Berlin-Dahlem, Germany ( lab head ) (1)
Department of Cell Biology and Histology, Faculty of Medicine, Campus Mare Nostrum,University of Murcia, 30100 Murcia, IMIB, Spain (1)
Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark (1)
Ludwig-Maximilians-Universität-München Großhaderner Straße 2 D-82152 Planegg-Martinsried (1)
MPIs for Biophysics and Brain Research (1)
Max Planck Institute of Biophysics and Max Planck Institute for Brain Research (1)
Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry (1)
School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia (1)
The Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China. (1)
The Second Clinical Medical College of Jinan University (Shenzhen People’s Hospital), Shenzhen 518020, China (1)
University of Zurich, Switzerland (1)

Tags

xref:PubMed:22962679 (1)

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A fluorogenic, peptide-based probe for the detection of Cathepsin D in macrophages.

Not available

S-EPMC10622513 | biostudies-literature

Integrated omics analysis reveals metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass

ORGANISM(S): Hungateiclostridium Thermocellum (ncbitaxon:1515)

MSV000080128 | MassIVE

ORC2 S2-DSRC ChIP-Seq experiment

modENCODE_submission_2753 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known ...

ORGANISM(S): Drosophila melanogaster

2010-03-16 | E-GEOD-20887 | biostudies-arrayexpress

Arabidopsis thaliana strain:Col-0 Epigenomics

Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. We performed whole genome bisulfite sequencing to assess the spatio-temporal dyna...

ORGANISM(S): Arabidopsis thaliana

2015-05-02 | E-MTAB-4211 | biostudies-arrayexpress

Renal oncocytoma characterized by the defective complex I of the respiratory chain boosts the synthesis of the ROS scavenger glutathione

Renal oncocytomas are rare benign tumors of the kidney and are characterized by a deficient complex I (CI) enzyme activity of the oxidative phosphorylation (OXPHOS) system caused by mitochondrial DNA (mtDNA) mutations. Yet, little is known about the underlying molecular mechanisms and alterations of...

ORGANISM(S): Homo sapiens (Human)

2017-11-21 | PXD007633 | Pride

Renal oncocytoma - complex i deficiency - glutathione metabolism - mtdna mutation

ORC2 ML-DmBG3-c2 ChIP-Seq experiment

modENCODE_submission_2754 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known ...

ORGANISM(S): Drosophila melanogaster

2010-03-16 | E-GEOD-20888 | biostudies-arrayexpress

Synthesis by extrusion: continuous, large-scale preparation of MOFs using little or no solvent.

Not available

S-EPMC5639793 | biostudies-literature

Transcription profiling of Arabidopsis cells cultures undergoing transdifferentiation

The formation of vascular tissue occurs when cellulose, hemicellulose, lignin and other wall components are deposited within the primary cell wall. These secondary thickened cells then undergo programmed cell death producing a network of empty cells with which water and ions can be transported thro...

ORGANISM(S): Arabidopsis thaliana

2008-06-14 | E-GEOD-6148 | biostudies-arrayexpress

SSH-PCR dehydrated supraoptic nucleus

The magnocellullar neurons (MCNs) of the supraoptic nucleus (SON) of the hypothalamus are the principle source of the neuropeptide hormone vasopressin (VP), which has a crucial role in osmoregulation. Physiological activation of the SON by dehydration results is a massive release of VP from stores i...

ORGANISM(S): Rattus norvegicus

2010-06-30 | E-GEOD-3132 | biostudies-arrayexpress

Cascading effects of root microbial symbiosis on the development and metabolome of the insect herbivore Manduca sexta L

Root mutualistic microbes can modulate the production of plant secondary metabolites affecting plant–herbivore interactions. Still, the main mechanisms underlying the impact of root mutualists on herbivore performance remain ambiguous. In particular, little is known about how changes in the plant...

2023-09-12 | MTBLS2700 | MetaboLights

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