Zhang David D - OmicsDI

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Unknown (791)
Transcriptomics (154)
Genomics (110)
Proteomics (107)
Metabolomics (17)
Models (2)
Genomic (2)
Multiomics (1)

Organisms

Homo sapiens (207)
Mus musculus (69)
Arabidopsis thaliana (12)
Saccharomyces cerevisiae (8)
Escherichia coli (6)
Rattus norvegicus (5)
Drosophila melanogaster (3)
Zea mays (2)
Triticum aestivum (2)
Populus x canadensis (1)
Gasterosteus aculeatus (1)
Sorghum bicolor (1)
Mus musculus domesticus (1)
Xenopus laevis (1)
Medicago truncatula (1)
Oryza sativa (1)
Pseudomonas putida (1)
Ovis aries (1)
Mus (1)
Rattus rattus (1)
Chlamydomonas reinhardtii (1)
Coronaviridae sp. (1)
Petunia x hybrida (1)
Pocillopora verrucosa (1)
Staphylococcus aureus subsp. aureus NCTC 8325 (1)
Ustilaginoidea virens (1)

Organisms

Arabidopsis thaliana (1)

Repository

biostudies-arrayexpress (173)
EGA (89)
pride (51)
MassIVE (35)
MetaboLights (14)
PeptideAtlas (10)
PanoramaPublic (4)
GNPS (3)
iProX (3)
jPOST (3)
BioModels (2)
dbGaP (2)
ENA (2)
geo (1)
PAXDB (1)

Tissue

Cell culture (15)
Brain (7)
Blood plasma (4)
Blood (3)
Blood cell (3)
Blood serum (3)
Lung (3)
Mesenchymal cell (3)
Bone marrow (2)
Epithelial cell (2)
Kidney (2)
Leaf (2)
Neutrophil (2)
Pancreas (2)
T cell (2)
Adipose tissue (1)
Bile (1)
Bile duct (1)
Blood-lymph (1)
Cardiac muscle cell (1)
Colon (1)
Colon endothelial cell (1)
Colon endothelium (1)
Corolla (1)
Eye (1)
Fat cell (1)
Fetal cardiomyocyte (1)
Gastric gland (1)
Heart (1)
Hippocampal neuron (1)

Disease

Colon cancer (3)
Brain cancer (2)
Breast cancer (2)
Disease free (2)
Bacterial infectious disease (1)
Acute leukemia (1)
Acute pancreatitis (1)
Alzheimer's disease (1)
Amyotrophic lateral sclerosis (1)
Brain ischemia (1)
Childhood extraosseous osteosarcoma (1)
Cholangiocarcinoma (1)
Chronic bronchitis (1)
Chronic kidney disease (1)
Embryonal rhabdomyosarcoma (1)
Eye disease (1)
Fibrosarcoma (1)
Gastric adenocarcinoma (1)
Head and neck cancer (1)
Lung cancer (1)
Lung carcinoma (1)
Malignant mesothelioma (1)
Melanoma (1)
Neuroblastoma (1)
Pancreatic cancer (1)
Pancreatitis (1)
Peripheral primitive neuroectodermal tumor (1)
Prostate adenocarcinoma (1)
Renal Wilms' tumor (1)
Renal cell carcinoma (1)

Technology Type

Mass Spectrometry (51)
Shotgun proteomics (27)
Mass spectrometry (13)
Bottom-up proteomics (10)
Data-independent acquisition (6)
Data-dependent acquisition (5)
Illumina HiSeq 2000 (2)
Illumina HiSeq 2000, Illumina_2.5M (2)
Illumina HiSeq 2500, ILLUMINA (2)
Affinity purification coupled with mass spectrometry proteomics (2)
Gel-based experiment (2)
SWATH MS (2)
Affymetrix 6.0 (1)
Affymetrix_U133v2, Illumina HiSeq 2000 (1)
Illumina 1.2M, Affymetrix 6.0 (1)
Illumina 2.5M, Illumina HiSeq 2000 (1)
Illumina HiSeq 2000, Illumina Genome Analyzer IIx (1)
Illumina HiSeq 2000, Illumina Infinium HumanMethylation450 BeadChip, Affymetrix expression array, ILLUMINA (1)
Illumina HiSeq 2500 (1)
Mass spectrometry assay (1)
NMR spectroscopy (1)
Affinity proteomics (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)
DiaPASEF (1)
MSE (1)
Top-down proteomics (1)

Instrument Platform

LTQ Orbitrap Velos (14)
Q Exactive (6)
LTQ FT (5)
Illumina NovaSeq 6000 (4)
Q Exactive HF (3)
Orbitrap Fusion Lumos (3)
Q Exactive Plus (3)
LTQ Orbitrap (3)
Liquid Chromatography MS - positive - reverse phase (3)
Illumina HiSeq 2000 (2)
Illumina HiSeq 4000 (2)
LTQ Orbitrap Elite (2)
Liquid Chromatography MS - negative - reverse phase (2)
FACSAria III (BD Sciences) (1)
HPC (1)
10x Genomics Chromium (1)
Illumina NovaSeq X (1)
Illumina HiSeq 2500 (1)
NextSeq 500 (1)
LTQ Orbitrap XL (1)
MaXis (1)
Exactive Plus (1)
Orbitrap Eclipse (1)
Orbitrap Exploris 480 (1)
TripleTOF 5600 (1)
TripleTOF 6600 (1)
5975C Series GC/MSD (Agilent) (1)
API 4000 QTRAP (AB Sciex) (1)
Agilent 5975E GC/MSD (Agilent) (1)
Bruker (1)

Publication Date

2014 (27)
2013 (25)
2011 (25)
2012 (21)
2015 (20)
2022 (18)
2010 (18)
2008 (18)
2026 (14)
2017 (14)
2016 (12)
2021 (11)
2024 (10)
2023 (10)
2020 (9)
2018 (8)
2025 (7)
2019 (5)
2007 (4)
2009 (3)
2005 (2)
2006 (2)
2004 (2)
2002 (1)

UNIPROT ID/AC

O00187 (1)
P01024 (1)
P02741 (1)
P04003 (1)
P06681 (1)
P0C0L4 (1)
P0C0L5 (1)
Q15485 (1)
10116.ENSRNOP00000000015 (1)
10116.ENSRNOP00000000222 (1)
10116.ENSRNOP00000000447 (1)
10116.ENSRNOP00000000791 (1)
10116.ENSRNOP00000001467 (1)
10116.ENSRNOP00000002904 (1)
10116.ENSRNOP00000003622 (1)
10116.ENSRNOP00000003646 (1)
10116.ENSRNOP00000004127 (1)
10116.ENSRNOP00000004997 (1)
10116.ENSRNOP00000005601 (1)
10116.ENSRNOP00000005854 (1)
10116.ENSRNOP00000006385 (1)
10116.ENSRNOP00000006566 (1)
10116.ENSRNOP00000006672 (1)
10116.ENSRNOP00000006851 (1)
10116.ENSRNOP00000006978 (1)
10116.ENSRNOP00000008094 (1)
10116.ENSRNOP00000008328 (1)
10116.ENSRNOP00000008592 (1)
10116.ENSRNOP00000008848 (1)
10116.ENSRNOP00000008851 (1)

ENSEMBL ID

ENSMUSG00000057465 (5)
ENSMUSG00000072849 (5)
ENSMUSG00000076586 (1)
ENSMUSG00000076591 (1)
ENSMUSG00000076695 (1)
ENSMUSG00000094546 (1)
ENSMUSG00000094652 (1)
ENSMUSG00000094930 (1)
ENSMUSG00000096833 (1)
ENSMUSG00000098814 (1)
ENSMUSP00000141097 (1)

CHEBI ID

CHEBI:30769 (6)
CHEBI:30915 (6)
CHEBI:16708 (5)
CHEBI:16811 (5)
CHEBI:17750 (5)
CHEBI:17992 (5)
CHEBI:18012 (5)
CHEBI:25017 (5)
CHEBI:29016 (5)
CHEBI:15428 (4)
CHEBI:15741 (4)
CHEBI:15756 (4)
CHEBI:15891 (4)
CHEBI:16010 (4)
CHEBI:16449 (4)
CHEBI:17151 (4)
CHEBI:17268 (4)
CHEBI:17368 (4)
CHEBI:17754 (4)
CHEBI:22653 (4)
CHEBI:26986 (4)
CHEBI:27570 (4)
CHEBI:27693 (4)
CHEBI:28300 (4)
CHEBI:28842 (4)
CHEBI:32816 (4)
CHEBI:6650 (4)
CHEBI:15354 (3)
CHEBI:18132 (1)
CHEBI:506227 (1)

Metabolite Name

3-phosphoglycerate (2)
Adenine (2)
Alanine (2)
Arginine (2)
Beta-Sitosterol (2)
Campesterol (2)
Cholesterol (2)
Cystathionine (2)
Cysteine (2)
Cystine (2)
Glucose (2)
Glutamine (2)
Glycerol (2)
Glycine (2)
Histidine (2)
Isoleucine (2)
Leucine (2)
Leucine (2)
Lysine (2)
Maltose (2)
Mannose (2)
Methionine (2)
Methyllysine (2)
Myo-inositol (2)
N-acetylalanine (2)
Phenylalanine (2)
S-adenosylmethionine (2)
Serine (2)
Succinate (2)
Threonine (2)

First Public Date

2025 (1)
2014 (1)

Modelling Approach

Ordinary differential equation model (2)

Lab affiliation

Agronomy College, Henan Agricultural University, China (2)
Department of Orthopaedics, Peking University Third Hospital (2)
Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, China 518055. (2)
The Walter and Eliza Hall Institute (2)
Tianjin Medical University General Hospital (2)
WEHI (2)
Analytical Chemistry Core Lab (ACL) – Proteomics Unit King Abdullah University of Science and Technology (KAUST) Thuwal, 23955-6900, Kingdom of Saudi Arabia (1)
CECAD, Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital of Cologne (1)
Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia. (1)
Charles Perkins Centre, The University of Sydney (1)
College of Plant Science and Technology, Huazhong Agricultural University (1)
Conway Institute Research Fellow Special Lecturer in Clinical Pharmacology School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland. (1)
David Meierhofer, MS facility, Max Planck Institute for Molecular Genetics, Berlin-Dahlem, Germany ( lab head ) (1)
Denes Hnisz, PhD Dept. of Genome Regulation Max Planck Institute for Molecular Genetics Ihnestraße 63-73 14195 Berlin, Germany (1)
Department of Biochemistry and Pharmacology, The Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville Victoria 3052, Australia (1)
Department of Biochemistry and Pharmacology, The Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Melbourne, Australia (1)
Department of Biology, Washington University-St. Louis St. Louis, Missouri 63130 USA (1)
Department of Clinical Laboratory, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R.China (1)
Department of Medical Genetics, University of British Columbia, Vancouver, Canada (1)
Department of Oncology, The Johns Hopkins University School of Medicine's Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA (1)
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. (1)
Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (1)
Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Department of Health and Human Services, Unites States Government (1)
Institute of Basic Medical Sciences, Xiyuan hospital China Academy of Chinese Medical Sciences (1)
Institute of Integrative Biology Biosciences Building Crown Street University of Liverpool Liverpool L69 7ZB UK (1)
Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom (1)
Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China (1)
Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V. (1)
MRC - Laboratory of Molecular Biology (1)
Professor of Biological Chemistry, Dept of Biochemistry, Institute of Integrative Biology, University of Liverpool. (1)

IsPrivate

False (2)

Submitter Keywords

Immuno-oncology (1)

Study type

Transcription profiling by array (105)
RNA-seq of coding RNA (25)
ChIP-seq (19)
ChIP-chip by tiling array (6)
RNA-seq of non coding RNA (4)
Comparative genomic hybridization by array (3)
ChIP-chip by array (2)
RNA-seq of coding RNA from single cells (2)
Transcription profiling by SAGE (1)
Transcription profiling by tiling array (1)
Spatial transcriptomics by high-throughput sequencing (1)
Other (1)
Single nucleus RNA sequencing (1)
Genotyping by high throughput sequencing (1)

Release Date

2022 (99)
2021 (97)
2025 (89)
2023 (78)
2024 (66)
2020 (64)
2019 (60)
2014 (50)
2015 (49)
2017 (45)
2011 (41)
2013 (36)
2012 (34)
2018 (33)
2016 (31)
2010 (29)
2026 (27)
2008 (14)
2009 (12)
2007 (6)
2005 (2)
2003 (2)

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Transcription profiling of Arabidopsis ALys RLK1 mutant reveals LysM receptor-like kinase mediates chitin perception and fungal resistance

A LysM Receptor-like Kinase Mediates Chitin Perception and Fungal Resistance in Arabidopsis; Jinrong Wan,1 Xuecheng Zhang,1 David Neece,2 Katrina M. Ramonell,3 Steve Clough,2,4 Sung-yong Kim,1 Minviluz Stacey,1 and Gary Stacey1*; 1Division of Plant Sciences, National Center for Soybean Biotechnology...

ORGANISM(S): Arabidopsis thaliana

2008-06-16 | E-GEOD-8319 | biostudies-arrayexpress

NEIGHBOR Consortium Glaucoma GWAS

This is a case-control study of primary open angle glaucoma (POAG). POAG is an intraocular pressure (IOP) related progressive optic neuropathy that ultimately leads to blindness. For this study we have formed a collaborative consortium contributing 2170 POAG cases and 2347 controls with a unified...

phs000238 | dbGaP

Profiling of sex-biased expression in Drosophila species

Extensive sex-biased expression has been seen in multiple surveys D. melanogaster. We were interested in broadly sampling sex-biased expression of orthologs and species- or lineage-specific genes in the Drosophila genus. To appropriately assay gene expression in multiple species, we used custom micr...

ORGANISM(S): Drosophila melanogaster

2007-11-07 | E-GEOD-6640 | biostudies-arrayexpress

Eftimie2010 - immunity to melanoma

The paper describes a model of immunity to melanoma. Created by COPASI 4.25 (Build 207) This model is described in the article: Modeling anti-tumor Th1 and Th2 immunity in the rejection of melanoma Raluca Eftimie, Jonathan L. Bramson, David J.D. Earn Journal of Theoretical Biology 265 (2010) 4...

2024-09-02 | BIOMD0000000768 | BioModels

Immuno-oncology

mRNA-Seq of whole flies from Drosophila

We sequenced mRNA from whole flies of females and male of Drosophila melanogaster, D. simulans, D. yakuba, D. ananassae, D. pseudobscura, D. mojavensis, and D. virilis as part of the modENCODE project to validate novel gene models found in D. melanogaster, identify genes differentially expressed bet...

ORGANISM(S): Drosophila melanogaster

2011-03-23 | E-GEOD-28078 | biostudies-arrayexpress

National Eye Institute Glaucoma Human Genetics Collaboration (NEIGHBOR) Consortium Glaucoma Genome-Wide Association Study

phs000238.v1.p1 | EGA

Vitamin D inhibits TNF-α induced apoptosis of human nucleus pulposus cells through regulation of NF-kB signaling pathway.

Not available

S-EPMC8237490 | biostudies-literature

Vitamin D receptor, an important transcription factor associated with aldosterone-producing adenoma.

Not available

S-EPMC3869669 | biostudies-literature

Expanded description and distribution of <i>Opisthotropis tamdaoensis</i> Ziegler, David & Vu, 2008 (Squamata, Natricidae), first record from Yunnan Province of China.

Not available