Ray P P - OmicsDI

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Unknown (15867)
Transcriptomics (1570)
Proteomics (207)
Genomics (106)
Metabolomics (83)
Genomic (12)
Models (2)
Other (2)
Clinical (1)

Organisms

Homo sapiens (524)
Danio rerio (258)
Mus musculus (244)
Salmo salar (77)
Oncorhynchus mykiss (77)
Pimephales promelas (40)
Rattus norvegicus (27)
Sparus aurata (15)
Arabidopsis thaliana (15)
Fundulus heteroclitus (14)
Oncorhynchus nerka (13)
Gadus morhua (13)
Carassius auratus (12)
Micropterus salmoides (11)
Solea senegalensis (11)
Saccharomyces cerevisiae (10)
Anguilla anguilla (10)
Dictyostelium discoideum (10)
Gasterosteus aculeatus (9)
synthetic construct (9)
Thermus thermophilus HB8 (8)
Scophthalmus maximus (7)
Oryzias latipes (7)
Hypomesus transpacificus (6)
Aliivibrio salmonicida LFI1238 (6)
Xenopus laevis (6)
Salmo trutta (5)
Paralichthys olivaceus (5)
Cyprinus carpio (5)
Oryza sativa (5)

Organisms

Homo sapiens (8)
Mus musculus (6)
Pinctada maxima (1)
Plasmodium falciparum 3D7 (1)
Ruditapes philippinarum (1)
Pseudomonas aeruginosa PAO1 (1)
Rattus norvegicus (1)
Populus trichocarpa (1)

Repository

biostudies-arrayexpress (1609)
pride (118)
MetaboLights (78)
EGA (36)
ENA (32)
MassIVE (25)
PAXDB (16)
PeptideAtlas (16)
geo (15)
dbGaP (12)
iProX (9)
jPOST (7)
PanoramaPublic (6)
GNPS (5)
BioModels (2)

Tissue

Cell culture (11)
Blood plasma (8)
Brain (7)
Blood serum (4)
Epithelial cell (4)
Plant cell (3)
Heart (3)
Permanent cell line cell (3)
Blood cell (3)
Root (2)
HeLa cell (2)
Testis (2)
Spleen (2)
Leaf (2)
Hepatocyte (2)
Blood (2)
Paw (1)
Peritoneal fluid (1)
Astrocyte of the cerebral cortex (1)
Neuron of cerebral cortex (1)
Skeletal muscle fiber (1)
Skeletal muscle myoblast (1)
Fungal cell (1)
Pluripotent stem cell (1)
Tissue (1)
Hypothalamus (1)
Thyroid gland (1)
Electrically active cell (1)
Embryonic stem cell (1)
Lymph node (1)

Disease

Normal (6)
Disease free (3)
Prostate cancer (2)
Rheumatoid arthritis (2)
Breast cancer (2)
Cardiovascular system disease (2)
COVID-19 (2)
Toxicity (1)
Mantle cell lymphoma (1)
Chronic lymphocytic leukemia (CLL) (1)
Ependymoma (1)
HIV (1)
Metastatic prostate cancer (1)
Schizophrenia (1)
Erythroleukemia (1)
Malignant fibrous histiocytoma (1)
Small cell lung cancer (1)
Acute lymphoblastic leukemia (1)
Locally advanced rectal cancer (1)
Burkitt lymphoma (1)
Head and neck squamous cell carcinoma (1)
Adenoid cystic carcinoma (1)
C. burnetii infected (1)
Prostate carcinoma (1)
Lung cancer (1)
Adenocarcinoma (1)
Healthy (1)
Central nervous system cancer (1)
Cancer-Bowel-Back passage (rectum) or large bowel (colon) (1)
Esophageal adenosquamous carcinoma (1)

Technology Type

Mass Spectrometry (118)
Shotgun proteomics (53)
Mass spectrometry (46)
Bottom-up proteomics (26)
Mass spectrometry assay (17)
NMR spectroscopy (14)
Affinity purification coupled with mass spectrometry proteomics (14)
Chemical cross-linking coupled with mass spectrometry proteomics (14)
Gel-based experiment (13)
Data-dependent acquisition (10)
Data-independent acquisition (9)
MSE (6)
Top-down proteomics (4)
HDMSE (3)
SWATH MS (3)
SRM/MRM (2)
Illumina HiSeq 2000 (1)
NMR spectroscopy assay (1)
SomaScan affinity proteomics (1)
All-ion fragmentation (1)
DiaPASEF (1)

Instrument Platform

Illumina NovaSeq 6000 (54)
Illumina HiSeq 4000 (30)
NextSeq 500 (16)
Illumina HiSeq 2500 (13)
Illumina NovaSeq X (10)
Illumina MiSeq (8)
Illumina HiSeq 2000 (8)
Agilent High resolution C scanner (4)
Genepix (4)
NextSeq 550 (4)
Dell PowerEdge R750; CPU: 2 × Intel Xeon Gold 6346 (32 Cores / 64 Threads); RAM: 188 GB (3)
TruSeq RNA Sample Preparation protocol (3)
HiSeq X Ten (3)
Tru-cut biopsy needle (Marquee®, 16 G × 10 cm) (2)
See manuscript (2)
NucleoSpin RNA/Protein kit lysis buffer (350 µL per tube; Macherey‑Nagel). (2)
. (2)
Other (2)
GenePix 4000B [Axon Instruments] (2)
Ion Torrent Proton (2)
Maxwell® RSC 48 Instrument (Promega, AS8500) (1)
Transrectal ultrasound-guided systematic sampling of prostate tissue (TRUS biopsy) (1)
Chromium Controller with Chromium Next GEM Single Cell 5’ and V(D)J (kits v1.1) (1)
TruSeq PCR-free Sample Preparation Kit (1)
Qiagen RNEasy Mini ki (1)
BD FACSAriaIIu cell sorter (1)
Poly-T oligo-attached magnetic beads (1)
TruSeq Stranded Total RNA Library Prep Gold Kit, TruSeq Stranded Total RNA Globin Kit (1)
Faxitron 43855-D irradiator (1)
FastPrep‑24 homogenizer (MP Biomedicals) (1)

Publication Date

2010 (292)
2013 (211)
2014 (200)
2011 (170)
2012 (169)
2015 (163)
2016 (93)
2026 (74)
2008 (72)
2025 (54)
2024 (45)
2022 (45)
2009 (45)
2023 (42)
2021 (42)
2019 (33)
2018 (30)
2017 (29)
2020 (28)
2007 (21)
2005 (20)
2006 (14)
2004 (5)
2002 (2)

UNIPROT ID/AC

Q7ZVT2_DANRE (15)
F6NP87_DANRE (15)
7955.ENSDARP00000111175 (15)
Q6GQM1_DANRE (15)
F1QSE1_DANRE (15)
7955.ENSDARP00000107930 (15)
7955.ENSDARP00000111194 (15)
7955.ENSDARP00000107946 (15)
Q7T334_DANRE (15)
Q6DHI9_DANRE (15)
7955.ENSDARP00000106634 (15)
A2BHA3_DANRE (15)
Q6NZZ2_DANRE (15)
A0A0R4IK21_DANRE (15)
F1QK60_DANRE (15)
7955.ENSDARP00000100434 (15)
E7F5A4_DANRE (15)
Q6IQX2_DANRE (15)
Q6GQM9_DANRE (15)
Q5BJ11_DANRE (15)
RS7_DANRE (15)
Q7T3G2_DANRE (15)
Q8JHI0_DANRE (15)
Q6PC80_DANRE (15)
Q803W9_DANRE (15)
P32581 (1)
P21190 (1)
P53438 (1)
P39001 (1)
P38615 (1)

ENSEMBL ID

ENSDARP00000125163 (16)
ENSDARP00000123922 (16)
ENSDARP00000116010 (16)
ENSDARP00000097050 (16)
ENSDARP00000087462 (16)
ENSDARP00000061164 (16)
ENSDARP00000000221 (16)
ENSDARG00000092233 (16)
ENSDARG00000092126 (16)
ENSDARG00000087390 (16)
ENSDARG00000079782 (16)
ENSDARG00000079564 (16)
ENSDARG00000075758 (16)
ENSDARG00000074289 (16)
ENSDARG00000071430 (16)
ENSDARG00000070083 (16)
ENSDARG00000068992 (16)
ENSDARG00000063908 (16)
ENSDARG00000058371 (16)
ENSDARG00000058358 (16)
ENSDARG00000056248 (16)
ENSDARG00000055996 (16)
ENSDARG00000055649 (16)
ENSDARG00000051783 (16)
ENSDARG00000046106 (16)
ENSDARG00000045180 (16)
ENSDARG00000045143 (16)
ENSDARG00000045014 (16)
ENSDARG00000044976 (16)
ENSDARG00000044975 (16)

CHEBI ID

CHEBI:15428 (21)
CHEBI:16919 (21)
CHEBI:15741 (20)
CHEBI:16449 (17)
CHEBI:78320 (17)
CHEBI:15891 (16)
CHEBI:15354 (16)
CHEBI:32816 (16)
CHEBI:16737 (16)
CHEBI:27266 (16)
CHEBI:24898 (16)
CHEBI:17268 (15)
CHEBI:30769 (15)
CHEBI:28044 (15)
CHEBI:15756 (14)
CHEBI:17754 (14)
CHEBI:26986 (14)
CHEBI:16811 (14)
CHEBI:17750 (13)
CHEBI:16704 (13)
CHEBI:28300 (13)
CHEBI:25017 (13)
CHEBI:15366 (12)
CHEBI:16828 (12)
CHEBI:17596 (12)
CHEBI:17822 (12)
CHEBI:28842 (11)
CHEBI:17895 (11)
CHEBI:17295 (11)
CHEBI:17351 (11)

Metabolite Name

Creatine (20)
Creatinine (19)
L-Phenylalanine (18)
Choline (17)
Betaine (14)
Valine (13)
Adenosine (13)
Glycine (13)
Taurine (13)
Xanthine (13)
L-Tryptophan (12)
Uracil (12)
Glucose (12)
Uridine (12)
Leucine (11)
Methionine (11)
Tyrosine (11)
Alanine (11)
Threonine (11)
Sarcosine (11)
Isoleucine (11)
Hypoxanthine (11)
Adenine (11)
Guanine (11)
L-Glutamine (11)
L-Leucine (11)
Inosine (11)
L-Tyrosine (10)
Glutamine (10)
Citrate (10)

First Public Date

2024 (6)
2021 (5)
2014 (5)
2025 (4)
2019 (3)
2022 (2)
2020 (2)
2018 (2)
2023 (1)
2017 (1)
2015 (1)

Modelling Approach

Ordinary differential equation model (1)

Study status

Terminated (1)

Lab affiliation

Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto (2)
Virginia Tech, Department of Biochemistry (2)
Professor, Molecular Medicine Scientific Director UF Scripps Biomedical Research University of Florida (2)
Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720 (2)
Department of Animal and Poultry Sciences and the School of Neuroscience, Virginia Tech, Blacksburg, VA, USA (2)
Faculty of Chemistry, Biotechnology and Food Science Norwegian University of Life Sciences Post Office Box 5003 1432, Ås Norway (2)
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands (2)
Sichuan University (2)
University of Victoria (2)
Physiology & Pharmacology, Cumming School of Medicine, University of calgary, Cagary (1)
Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Barcelona, Spain (1)
Newcastle University Biosciences Institute Newcastle upon Tyne NE1 7RU (1)
Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen Key Laboratory of Translational Medicine of Tumor, International Cancer Center, Department of Cell Biology and Genetics, School of Medicine, Shenzhen University, Shenzhen, 518055, China. (1)
IWE ZIK HALOmem, Martin Luther University Halle-Wittenberg, Halle, Germany (1)
Departments of Radiation Oncology, The University of Michigan Medical School, Ann Arbor, Michigan 48109. (1)
Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany (1)
Institute of Microbiology of the CAS, Czech Republic (1)
Department of Animal and Poultry Sciences, Virginia Tech., Blacksburg, VA, USA (1)
Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China (1)
Professor and Director, School of Neuroscience, Virginia Tech., Blacksburg, VA, USA (1)
Lu Qingtao, Ph.D. Photosynthesis Research Center, Room 230 Institute of Botany, CAS Haidian Xiangshan Nanxincun 20# Beijing. 100093 Phone, +86-10-62836254 Email, lu_qingtao@ibcas.ac.cn (1)
Washington University, Department of Medicine, Division of Pulmonary and Critical Care (1)
Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK (1)
Proteomics Service CIC bioGUNE Bizkaia Tec. Park Build. 800 48160 Derio (Spain) (1)
CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China (1)
Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copehagen, Denmark (1)
McKetta Department of Chemical Engineering, The University of Texas at Austin, USA (1)
Dr. Sanjeeva Srivastava, Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India (Lab head). (1)
1. Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan. 2. Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan. 3. Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Linkou 33305, Taiwan. 4. Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 33302, Taiwan. (1)
LSMBO - IPHC - CNRS (1)

IsPrivate

False (2)

Model Flag

Non Kinetic (1)

Classification

protozoa (1)
bacteria (1)

Modification

57.02146 (2)
15.99491 (2)
0.984 (1)

Study type

Transcription profiling by array (1155)
RNA-seq of coding RNA (138)
Comparative genomic hybridization by array (91)
Unknown experiment type (52)
ChIP-seq (24)
Genotyping by array (17)
Methylation profiling by array (15)
RNA-seq of coding RNA from single cells (15)
RNA-seq of non coding RNA (15)
Other (14)
Proteomic profiling by array (10)
DNA-seq (9)
RNA-seq of total RNA (7)
Animal - High-throughput sequencing (6)
ChIP-chip by array (5)
MicroRNA profiling by array (5)
ChIP-chip by tiling array (4)
Methylation profiling by high throughput sequencing (4)
Animal - One-color microarray (3)
Transcription profiling by RT-PCR (3)
Cell line - High-throughput sequencing (2)
Transcription profiling by tiling array (2)
Ribo-seq (2)
Transcription profiling by SAGE (1)
Human - Two-color microarray (1)
MicroRNA profiling by high-throughput sequencing (1)
Animal - Single-cell sequencing (1)
Human - High-throughput sequencing (1)
Spatial transcriptomics by high-throughput sequencing (1)
ATAC-seq (1)

Release Date

2022 (1813)
2021 (1669)
2023 (1660)
2025 (1613)
2024 (1407)
2020 (1385)
2019 (1107)
2018 (963)
2015 (732)
2017 (731)
2016 (696)
2014 (588)
2010 (555)
2013 (519)
2012 (483)
2011 (449)
2026 (278)
2009 (276)
2008 (202)
2007 (99)
2006 (76)
2005 (70)
2004 (27)
2001 (23)
2003 (21)
2002 (17)
2000 (6)
1999 (4)
1998 (3)
1997 (2)

Location

Australia (1)

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A metabolite roadmap of the wood-forming tissue in Populus tremula (UPLC-MS assay; Wood fibre and ray cell tissue)

Wood, or secondary xylem, is the product of xylogenesis, a developmental process that begins with the proliferation of cambial derivatives and ends with mature xylem fibers and vessels with lignified secondary cell walls. Fully mature xylem has undergone a series of cellular processes, including ...

2020-09-01 | MTBLS1831 | MetaboLights

X-ray Irradiation Suppresses Keloid Growth by Inducing G2/M Arrest via the Phytosphingosine-KIF20A Axis

Keloid radiotherapy is clinically effective but has an incomplete underlying molecular mechanism and limited accessibility; we used X-ray exposure to identify effector pathways replicating its antifibrotic benefits without further radiation. After collecting patient keloid samples, primary human kel...

2026-06-06 | MTBLS14461 | MetaboLights

Characterization of protoporphytin IX effects on X-ray irradiation in Hela cells in vitro

Hela cells were used to evaluate the protoporphytin IX (PpIX) effects on X-ray irradiation. Treatment conditions were (1) control group (untreated cells); (2) cells treated with 1 Œºg /ml PpIX for 6 hours; (3) cells irradiated with 3Gy X-rays; (4) cells treated with 1 Œºg /ml PpIX for 6 hours prior ...

ORGANISM(S): Homo sapiens

2015-01-21 | E-GEOD-61805 | biostudies-arrayexpress

Sensory ray genes

These experiments were undertaken with the goal of identifying genes whose expression is enriched in or restricted to the sensory rays of the C. elegans male tail. We constructed two mutant strains in which ray development is either compromised (EM672) or enhanced (EM673), and harvested mRNA from ad...

ORGANISM(S): Caenorhabditis elegans

2006-01-05 | E-GEOD-3979 | biostudies-arrayexpress

Expression profiles of X-ray responsive miRNA in human cells [miRNA data]

MicroRNA (miRNA) is a type of non-coding RNA that regulates the expression of its target genes by interacting with the complementary sequence of the target mRNA molecules. Recent evidence has shown that genotoxic stress induces miRNA expression, but the target genes involved and role in cellular res...

ORGANISM(S): Homo sapiens

2014-03-14 | E-GEOD-30130 | biostudies-arrayexpress

Structure of the metastatic factor P-Rex1 reveals a two-layered autoinhibitory mechanism

Rho GTPases regulate actin dynamics and cell motility, and their hyperactivation drives cancer metastasis1. P-Rex (PI(3,4,5)P3-dependent Rac Exchanger) guanine nucleotide exchange factors (GEFs) are potent on-switches for Rho GTPase signalling and are frequently dysregulated in metastatic cancer2. P...

ORGANISM(S): Homo sapiens (Human)

2022-08-12 | PXD034327 | Pride

Expression profiles of X-ray responsive miRNA in human cells

ORGANISM(S): Homo sapiens

2014-03-14 | E-GEOD-30132 | biostudies-arrayexpress

Expression data from human unbilical endothelial cells (HUVEC) irradiated with X-ray

To understand the molecular mechanism underlying inflammatory reaction in vascular system post exposure to ionizing radiation, we carried out microarray analysis in HUVEC exposed with X-ray HUVEC were irradiated with X-ray (2.5 Gy) and then cultured for 6, 12, and 24 hr. Total RNA were extracted fro...

ORGANISM(S): Homo sapiens

2016-01-21 | E-GEOD-76484 | biostudies-arrayexpress

Expression profiles of X-ray responsive miRNA in human cells [mRNA data]

'MicroRNA (miRNA) is a type of non-coding RNA that regulates the expression of its target genes by interacting with the complementary sequence of the target mRNA molecules. Recent evidence has shown that genotoxic stress induces miRNA expression, but the target genes involved and role in cellular re...

ORGANISM(S): Homo sapiens

2014-03-14 | E-GEOD-30131 | biostudies-arrayexpress

Endophyte-promoted Phosphorous Fixation in Poplar

Studying the endophyte strains of poplar that help the plant solubilize phosphate, we observed direct evidence of endophyte-promoted phosphorous fixation. Using synchrotron x-ray fluorescence (SR-XRF) microscopy combined with x-ray absorption near-edge structure (XANES), we visualized the nutrient p...

ORGANISM(S): Populus Trichocarpa (ncbitaxon:3694)

2020-01-29 | MSV000084860 | MassIVE

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