Clark D D - OmicsDI

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Unknown (4554)
Transcriptomics (703)
Genomics (97)
Proteomics (93)
Multiomics (14)
Metabolomics (13)
Models (2)
Other (1)

Organisms

Homo sapiens (323)
Mus musculus (215)
Drosophila melanogaster (41)
Arabidopsis thaliana (37)
Saccharomyces cerevisiae (26)
Rattus norvegicus (17)
Danio rerio (13)
Bos taurus (7)
Tetranychus urticae (6)
Sus scrofa (6)
Glycine max (5)
Caenorhabditis elegans (5)
Zea mays (4)
Mycobacterium tuberculosis (4)
Neurospora crassa (3)
Pseudomonas aeruginosa (3)
Nasonia giraulti (2)
Hevea brasiliensis (2)
Cryptopygus antarcticus (2)
Macaca mulatta (2)
Xenopus laevis (2)
Harpagifer antarcticus (2)
Schizosaccharomyces pombe (2)
Nasonia vitripennis (2)
Hordeum vulgare (2)
Solanum lycopersicum (2)
Mycobacterium tuberculosis H37Rv (2)
Oryza sativa Japonica Group (2)
Gallus gallus (2)
Oryctolagus cuniculus (1)

Organisms

Melospiza georgiana (3)
Passerculus sandwichensis (3)
Melospiza melodia melodia (3)
Drosophila melanogaster (2)
Drosophila simulans (1)
Ovis aries (1)
Arabidopsis thaliana (1)

Repository

biostudies-arrayexpress (751)
pride (50)
ENA (28)
MassIVE (26)
EGA (25)
PeptideAtlas (14)
MetaboLights (11)
BioModels (2)
GNPS (2)
PanoramaPublic (1)
PAXDB (1)

Tissue

Others (11)
Cell culture (9)
Epithelial cell (6)
Embryonic stem cell (4)
Plasma Non-glyco (3)
Brain (3)
HeLa cell (3)
Blood (2)
Blood plasma (2)
Kidney (2)
Monocyte (2)
Dental plaque (1)
Embryo (1)
Epithelial cell of prostate (1)
Fungal cell (1)
Heart (1)
Hyphal cell (1)
Kidney cell (1)
Kidney proximal convoluted tubule epithelial cell (1)
Leaf (1)
Liver (1)
Lung (1)
Neutrophil (1)
PBMC cell line (1)
Permanent cell line cell (1)
Plant cell (1)
Primary cell (1)
Primary neuron (1)
Retinal pigment epithelial cell (1)
Root (1)

Disease

Disease free (3)
HHV-6B infected (2)
XCGD (1)
Huntington's disease mouse model (1)
Metastatic colorectal cancer (1)
GIP-dependent Cushing's syndrome (1)
Small cell lung carcinoma (1)
Glioblastoma (1)
Neuroblastoma (1)
Adult respiratory distress syndrome (1)
Age related macular degeneration (1)
Alzheimer's disease (1)
Brain cancer (1)
Breast cancer (1)
Fibrolamellar carcinoma (1)
Prostate adenocarcinoma (1)
Prostate carcinoma (1)
Renal cell carcinoma (1)

Technology Type

Mass Spectrometry (50)
Shotgun proteomics (22)
Affinity purification coupled with mass spectrometry proteomics (11)
Mass spectrometry (10)
Bottom-up proteomics (10)
Data-dependent acquisition (5)
Gel-based experiment (4)
Data-independent acquisition (2)
SWATH MS (2)
Top-down proteomics (2)
Illumina Omni 2.5, Illiumina Omni 2.5 (1)
Illumina_Infinium_HumanMethylation450, Illumina_HumanHT-12v4 (1)
Mass spectrometry assay (1)
NMR spectroscopy (1)
All-ion fragmentation (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)
RNA mass spectrometry (1)

Instrument Platform

Illumina HiSeq 4000 (11)
NextSeq 500 (7)
Q Exactive Plus (7)
Q Exactive (6)
Illumina NovaSeq 6000 (5)
Illumina HiSeq 2000 (5)
LTQ Orbitrap (5)
Orbitrap Fusion Lumos (4)
Illumina HiSeq 2500 (3)
Illumina NovaSeq X (2)
NextSeq 550 (2)
SYNAPT G2-Si (2)
TSQ Altis (2)
Xevo G2 XS Tof (2)
Xevo G2-XS QTof (2)
LTQ (2)
Agilent Tapestation 4200 (1)
10x Chromium with a target of 5,000 cells. Chromium Single Cell 3’ Library & Gel Bead Kit v2 (1)
10X Genomics reagent kit (1)
Qiagen (1)
TruSeq Stranded mRNA Sample Preparation Kit (Illumina) (1)
ProScanArray Microarray Scanner [PerkinElmer] (1)
Illumina Genome Analyzer IIx (1)
418 [Affymetrix] (1)
NA (1)
Ion Torrent Proton (1)
GenePix 4000B (1)
HiSeq X Ten (1)
Illumina MiSeq (1)
Illumina HiSeq 1500 (1)

Publication Date

2015 (127)
2010 (124)
2012 (107)
2013 (99)
2014 (75)
2011 (63)
2016 (47)
2008 (30)
2009 (26)
2007 (21)
2022 (17)
2023 (16)
2025 (15)
2020 (14)
2021 (14)
2018 (13)
2024 (12)
2005 (9)
2026 (7)
2017 (6)
2004 (5)
2019 (4)
2006 (4)
2003 (1)

UNIPROT ID/AC

2711.XP_006464469.1 (1)
2711.XP_006464485.1 (1)
2711.XP_006464486.1 (1)
2711.XP_006465039.1 (1)
2711.XP_006465481.1 (1)
2711.XP_006465554.1 (1)
2711.XP_006465598.1 (1)
2711.XP_006465717.1 (1)
2711.XP_006465764.1 (1)
2711.XP_006466032.1 (1)
2711.XP_006466189.1 (1)
2711.XP_006466240.1 (1)
2711.XP_006466243.1 (1)
2711.XP_006466346.1 (1)
2711.XP_006466347.1 (1)
2711.XP_006466348.1 (1)
2711.XP_006466352.1 (1)
2711.XP_006466586.1 (1)
2711.XP_006467060.1 (1)
2711.XP_006467330.1 (1)
2711.XP_006467511.1 (1)
2711.XP_006468195.1 (1)
2711.XP_006468459.1 (1)
2711.XP_006468477.1 (1)
2711.XP_006468930.1 (1)
2711.XP_006468931.1 (1)
2711.XP_006469038.1 (1)
2711.XP_006469071.1 (1)
2711.XP_006469105.1 (1)
2711.XP_006469136.1 (1)

ENSEMBL ID

ENSG00000170477 (7)
ENSG00000229353 (3)
ENSG00000147251 (1)

CHEBI ID

CHEBI:15741 (5)
CHEBI:16449 (5)
CHEBI:15724 (4)
CHEBI:16027 (4)
CHEBI:16335 (4)
CHEBI:16411 (4)
CHEBI:16704 (4)
CHEBI:16750 (4)
CHEBI:16811 (4)
CHEBI:17154 (4)
CHEBI:17368 (4)
CHEBI:17596 (4)
CHEBI:17724 (4)
CHEBI:17750 (4)
CHEBI:18237 (4)
CHEBI:27897 (4)
CHEBI:28635 (4)
CHEBI:28867 (4)
CHEBI:29016 (4)
CHEBI:32816 (4)
CHEBI:133530 (3)
CHEBI:14314 (3)
CHEBI:15318 (3)
CHEBI:15354 (3)
CHEBI:15356 (3)
CHEBI:15428 (3)
CHEBI:15584 (3)
CHEBI:15611 (3)
CHEBI:15999 (3)
CHEBI:16040 (3)

Metabolite Name

Xanthine (5)
2-Hydroxycinnamic acid (3)
4-Hydroxybenzaldehyde (3)
Citramalic acid (3)
Dimethylglycine (3)
Ethylmalonic acid (3)
Hypoxanthine (3)
Isomaltose (3)
Mannitol (3)
Pantothenic acid (3)
Sebacic acid (3)
Suberic acid (3)
Uridine (3)
(R)-2,3-Dihydroxy-isovalerate (2)
(S)-3-Hydroxybutyric acid (2)
1-Hexylglycerol (2)
1-Methyl-6-phenyl-1H-imidazo[4,5-b]pyridin-2-amine (2)
11-Dehydrocorticosterone (2)
12-Methyltridecanoic acid (2)
2,4-Dihydroxybutanoic acid (2)
2,5-Dimethyl-1H-pyrrole (2)
2-(1-Ethoxyethoxy)propanoic acid (2)
2-(Ethylamino)-4,5-dihydroxybenzamide (2)
2-Aminoisobutyric acid (2)
2-Hydroxy-2-methylbutyric acid (2)
2-Hydroxy-3-methylbutyric acid (2)
2-Hydroxybutyric acid (2)
2-Hydroxymethylclavam (2)
2-Isopropylmalic acid (2)
2-Ketobutyric acid (2)

First Public Date

2023 (9)
2017 (8)
2024 (3)
2015 (3)
2014 (2)
2026 (1)
2020 (1)
2010 (1)

Modelling Approach

Constraint-based model (1)
Ordinary differential equation model (1)

Lab affiliation

Pacific Northwest National Laboratory (4)
University of Dundee, School of Life Sciences (4)
Pathology - Lab & Genomic Medicine (LGM); Washington University School of Medicine (3)
Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720 (2)
1 Garvan Institute of Medical Research and The Kinghorn Cancer Centre, 384 Victoria Street Darlinghurst Sydney, NSW, 2010, Australia. 2 St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia. (1)
Boston College (1)
CIR, Queen’s Medical Research Institute, University of Edinburgh (1)
CRUK - Beatson Institute for Cancer Research - Switchback Rd, Bearsden, Glasgow G61 1BD - United Kingdom (1)
CRUK Beatson Institute, Switchback Road, Glasgow G61 1BD, UK. (1)
Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, UK (1)
Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford; Oxford, U.K.; 3MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford; Oxford, U.K. (1)
Civil and Environmental Engineering, James H Clark Center Room E250, Stanford University, CA United States (1)
Department of Biochemistry and Cell Biology; Rice University; Houston, TX USA (1)
Department of Biomedicine, Aarhus University, Aarhus, Denmark STENO Diabetes Center Aarhus, Aarhus, Denmark (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 Oncology and Diagnostic Sciences, University of Maryland School of Dentistry, Baltimore MD (1)
Department of Oncology and Pathology, Karolinska Institute and Science for Life Laboratory (1)
Department of Oncology, The Johns Hopkins University School of Medicine's Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA (1)
Department of Plant Pathology University of California-Davis One Shield Avenue, Davis, CA 95616 (1)
Departments of Chemistry, Biological Sciences, Microbiology and Immunology, Vanderbilt University (1)
Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (1)
F.M Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA. Harvard Medical School, Boston, MA, USA (1)
Geriatrics and Gerontology, Department of Medicine, University of Wisconsin - Madison (1)
Helmholtz-Centre for Environmental Research - UFZ GmbH Department of Molecular Toxicology Permoserstrasse 15, 04318 Leipzig, Germany (1)
Host-Parasite Interactions Section, RML/NIAID/NIH (1)
Institute for Ophthalmic Research Eberhard-Karls University of Tuebingen Elfriede-Aulhorn-Str. 7 D-72076 Tuebingen. Germany. (1)
Institute of Cancer Research, London (1)
Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, TBP Lab (1)
La Trobe University (1)
Laboratoire de Spectrométrie de Masse Protéomique (LSMP), Institut Curie, PSL Research University, France (1)

IsPrivate

False (2)

Study type

Transcription profiling by array (434)
RNA-seq of coding RNA (114)
ChIP-chip by tiling array (31)
ChIP-seq (28)
Unknown experiment type (25)
Comparative genomic hybridization by array (21)
RNA-seq of non coding RNA (20)
Methylation profiling by high throughput sequencing (15)
Other (13)
Methylation profiling by array (11)
Transcription profiling by SAGE (8)
RNA-seq of coding RNA from single cells (8)
Animal - High-throughput sequencing (4)
Transcription profiling by tiling array (4)
Genotyping by array (2)
Proteomic profiling by array (2)
Baseline (1)
Human - High-throughput sequencing (1)
High-throughput sequencing (1)
ChIP-chip by array (1)
Transcription profiling by RT-PCR (1)
Bisulfite-seq (1)
DNA-seq (1)
Genotyping by high throughput sequencing (1)
RNA-seq of total RNA (1)

Release Date

2022 (508)
2021 (477)
2023 (451)
2025 (417)
2024 (398)
2020 (342)
2015 (295)
2019 (286)
2018 (267)
2016 (257)
2014 (243)
2013 (233)
2012 (223)
2017 (214)
2010 (198)
2011 (142)
2009 (96)
2008 (77)
2026 (60)
2007 (35)
2006 (31)
2005 (18)
2004 (14)
2002 (5)
2001 (5)
2003 (4)
2000 (4)
1999 (3)
1997 (1)
1996 (1)

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Subtractive Hybridization Reveals Novel Genes Associated with D. melanogaster Early Embryogenesis.

Background: The early stages of D. melanogaster embryogenesis involve cell migration and pattern formation, and lead to the formation of three germ layers (the ectoderm, mesoderm and endoderm). These developmental events are controlled by differential gene activity. In the current study we used a su...

ORGANISM(S): Drosophila melanogaster

2010-05-16 | E-GEOD-15000 | biostudies-arrayexpress

Role of Vitamin D in the Hygiene Hypothesis: The Interplay between Vitamin D, Vitamin D Receptors, Gut Microbiota, and Immune Response.

Not available

S-EPMC5179549 | biostudies-literature

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

Not available

S-EPMC3953205 | biostudies-literature

Seasonal Differences of 25-Hydroxyvitamin D Concentrations in Children and Adolescents from Mexico City and Metropolitan Area.

Not available

S-EPMC12011372 | biostudies-literature

Crystal Structure of a Complex of Surfactant Protein D (SP-D) and Haemophilus influenzae Lipopolysaccharide Reveals Shielding of Core Structures in SP-D-Resistant Strains.

Not available

S-EPMC4862711 | biostudies-literature

Molecular evolution, functional variation, and proposed nomenclature of the gene family that includes sphingomyelinase D in sicariid spider venoms.

Not available

S-EPMC2767091 | biostudies-literature

Low Serum Vitamin D Concentrations Are Associated with Insulin Resistance in Mexican Children and Adolescents.

Not available

S-EPMC6770751 | biostudies-literature

Airway Surfactant Protein D Deficiency in Adults With Severe Asthma.

Not available

S-EPMC4944769 | biostudies-literature

Evolutionary dynamics of origin and loss in the deep history of phospholipase D toxin genes.

Not available

S-EPMC6299612 | biostudies-literature

Effect of Carbon Dioxide on Neonatal Mouse Lung: A Genomic Approach

Rationale: Despite the deleterious effects associated with elevated carbon dioxide (CO2), or hypercapnia, it has been hypothesized that CO2 can protect the lung from injury. However, the effects of chronic hypercapnia on the neonatal lung are unknown. Objectives: To determine whether chronic hyperca...

ORGANISM(S): Mus musculus

2010-07-01 | E-GEOD-3161 | biostudies-arrayexpress

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5465 Results

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Organisms

Organisms

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Tissue

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CHEBI ID

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