Plant systems biology

Show results for

Unknown (8022)
Transcriptomics (674)
Genomics (381)
Proteomics (242)
Metabolomics (55)
Models (26)
Other (5)

Organisms

Arabidopsis thaliana (154)
Homo sapiens (120)
Mus musculus (78)
Oryza sativa (24)
Zea mays (22)
Saccharomyces cerevisiae (17)
Danio rerio (13)
Drosophila melanogaster (12)
Bos taurus (11)
Oryza sativa Indica Group (11)
Solanum lycopersicum (11)
Vitis vinifera (10)
Medicago truncatula (9)
Glycine max (8)
Oryza sativa Japonica Group (8)
Gallus gallus (6)
Hordeum vulgare (6)
Solanum tuberosum (6)
Arabidopsis (5)
Escherichia coli str. K-12 substr. MG1655 (5)
Triticum aestivum (5)
Olea europaea (4)
Schizosaccharomyces pombe (4)
Mycobacterium tuberculosis (4)
Mycobacterium tuberculosis H37Rv (4)
Rhodopirellula baltica (3)
Aspergillus niger (3)
Ostreococcus tauri (2)
Nicotiana tabacum (2)
Embryophyta (1)

Organisms

Arabidopsis thaliana (85)
Solanum tuberosum (8)
Oryza sativa (6)
Saccharum officinarum (5)
Zea mays (5)
Triticum aestivum (4)
Vitis vinifera (4)
Nicotiana benthamiana (3)
Medicago truncatula (3)
Marchantia polymorpha (3)
rhizosphere metagenome (3)
Agrobacterium tumefaciens (2)
Solanum lycopersicum (2)
wastewater metagenome (2)
Lotus japonicus (2)
Nicotiana tabacum (2)
Fusarium oxysporum f. sp. pisi (1)
Plasmodium falciparum 3D7 (1)
Aspergillus nidulans (1)
Neisseria meningitidis (1)
Ophrys fusca (1)
Dunaliella viridis (1)
Phlomis purpurea (1)
Limnospira indica PCC 8005 (1)
Quercus ilex (1)
Lactuca sativa var. capitata (1)
Cardamine sp. SIM-2007 (1)
Paramagnetospirillum magneticum AMB-1 (1)
Cylindrotheca closterium (1)
Methylorubrum extorquens (1)

Repository

biostudies-arrayexpress (682)
ENA (348)
pride (188)
MetaboLights (53)
MassIVE (28)
geo (24)
BioModels (20)
jPOST (12)
PAXDB (6)
Cell Collective (5)
PanoramaPublic (5)
GPMDB (4)
EGA (2)
GNPS (2)
iProX (2)
EVA (1)
FAIRDOMHub (1)

Tissue

Plant cell (55)
Leaf (41)
Root (25)
Cell culture (16)
Shoot (13)
Whole body (11)
Seedling (8)
Cell suspension culture (7)
Seed (6)
Photosynthetic cell (5)
Endosperm (4)
Flower bud (4)
Aleurone layer (3)
Protonema (3)
Rosette (3)
Embryo (3)
Nucleus (2)
Pitcher secretion (2)
Germ (2)
Plant cell line (2)
Cotyledon (2)
Root nodule (2)
Petiole (1)
Chloronema (1)
Caryopsis (1)
Pseudostem (1)
Exocrine glandular secretion (1)
Needle (1)
Berry (1)
Sprout (1)

Disease

Not Available (4)
Disease free (3)
Wounds and Injuries (3)
Type 1 diabetes mellitus (2)
Post-stasis (1)
Blumeria graminis hordei (powdery mildew) inoculation (1)
Squamous cell carcinoma has accession C0007137 in DiseaseStateDatabase NCI_Thesaurus (1)
Mock infected (1)
Acute myelomonocytic leukaemia (1)
Metarhizium anisopliae infected (1)
Head and neck squamous cell carcinoma (1)
Chicken Anaemia Virus infected (1)
Invasive ductal carcinoma (1)
Normal (1)
Tinea unguium (1)
Keratitis (1)
Tick borne (1)
Pneumonia (1)

Technology Type

Mass Spectrometry (188)
Shotgun proteomics (112)
Mass spectrometry (44)
Affinity purification coupled with mass spectrometry proteomics (27)
Bottom-up proteomics (22)
Data-dependent acquisition (18)
Mass spectrometry assay (9)
Gel-based experiment (9)
Top-down proteomics (5)
Chemical cross-linking coupled with mass spectrometry proteomics (5)
SWATH MS (5)
Data-independent acquisition (4)
NMR spectroscopy (1)
Metaproteomics (1)
SRM/MRM (1)

Instrument Platform

Illumina HiSeq 2000 (33)
Illumina NovaSeq 6000 (24)
Illumina HiSeq 2500 (21)
NextSeq 500 (12)
Illumina HiSeq 4000 (10)
NextSeq 550 (3)
ScanArray 5000 [PerkinElmer] (2)
Illumina Genome Analyzer II (2)
Microsyringe for intraperitoneal injection (1)
Computational server/cluster, Software: R (v4.3.x), Seurat package (v5.1.0) (1)
Biological safety cabinet, Centrifuge, Cell strainer, Automated cell counter/Hemocytometer (1)
Surgical dissection tools (1)
10X v3 (1)
Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis. (1)
Sequel II (1)
Illumina iScan microarray scanner (1)
BD Rhapsody system (1)
Chromium Single Cell 3’ Reagent kits v2 (1)
Agilent 2100 Bioanalyzer, Applied Biosystems 7900HT Sequence Detection System, Illumina TruSeq Small RNA Sample Preparation Kit (1)
RNeasy mini Kit, Ribo-Zero Human/Mouse/Rat kit (1)
Agilent Surescan High Resolution DNA microarray Scanner (1)
Illumina iScan (1)
Illumina iScan system (1)
QIAsymphony SP (1)
Nanodrop N1000 spectrophotometer (1)
Agilent Surescan High Resolution DNA Microarray Scanner (1)
454 GS FLX+ (1)
Agilent 2100 Bioanalyzer (1)
AB SOLiD 4 System (1)
BAS-1800 [FUJIFILM] (1)

Publication Date

2010 (98)
2015 (83)
2013 (75)
2014 (73)
2012 (73)
2011 (73)
2022 (52)
2024 (46)
2019 (46)
2016 (44)
2020 (41)
2021 (40)
2025 (37)
2017 (36)
2026 (33)
2023 (33)
2008 (33)
2018 (27)
2009 (25)
2005 (19)
2007 (16)
2006 (10)
2004 (2)
2003 (2)

UNIPROT ID/AC

Q9LKL2 (7)
Q93WK5 (5)
Q8L500 (5)
O81713 (5)
P92973 (3)
Q8F369_LEPIN (3)
Q8EYS5_LEPIN (3)
Q8F4C2_LEPIN (3)
EFG_LEPIN (3)
PURT_LEPIN (3)
RL22_LEPIN (3)
Q8F706_LEPIN (3)
Q8F9W7_LEPIN (3)
Q8F9C1_LEPIN (3)
Q9SQI2 (2)
Q9LIE5 (1)
O24646 (1)
Q9FFA7 (1)
Q9LTJ6 (1)
Q9FN03 (1)
Q8LGH4 (1)
Q9M086 (1)
Q9SYX2 (1)
P43254 (1)
Q94BT6 (1)
Q6R0H1 (1)
Q05609 (1)
Q0WPQ2 (1)
P49333 (1)
Q8LLV8 (1)

CHEBI ID

CHEBI:15428 (20)
CHEBI:15741 (18)
CHEBI:33699 (7)
CHEBI:18053 (5)
CHEBI:25078 (1)
CHEBI:35222 (1)
CHEBI:18153 (1)
CHEBI:22676 (1)
CHEBI:23530 (1)
CHEBI:58601 (1)
CHEBI:17969 (1)
CHEBI:57634 (1)
CHEBI:14314 (1)
CHEBI:17138 (1)
CHEBI:24636 (1)
CHEBI:48153 (1)
CHEBI:36080 (1)
CHEBI:15721 (1)
CHEBI:17797 (1)
CHEBI:16332 (1)
CHEBI:17363 (1)
CHEBI:18009 (1)
CHEBI:16474 (1)
CHEBI:28013 (1)
CHEBI:16526 (1)
CHEBI:16411 (1)
CHEBI:16108 (1)
CHEBI:18367 (1)
CHEBI:16761 (1)
CHEBI:15422 (1)

Metabolite Name

Glycerol (10)
Glycine (10)
Sucrose (9)
Fructose (9)
Myo-inositol (8)
Beta-alanine (8)
Glucose (8)
Phenylalanine (8)
Spermidine (8)
Cytosine (7)
Adenosine (7)
Malate (7)
Citrate (7)
Leucine (7)
Isoleucine (7)
Glutamine (7)
Alanine (7)
Threonine (7)
Tyramine (7)
Tyrosine (7)
Serine (7)
Adenine (7)
Arginine (7)
Phytosphingosine (6)
Urea (6)
Ribitol (6)
Uridine (6)
Xanthine (6)
Hypoxanthine (6)
Guanine (6)

First Public Date

2014 (60)
2025 (33)
2020 (32)
2023 (29)
2022 (29)
2017 (27)
2021 (24)
2026 (23)
2018 (22)
2013 (20)
2024 (15)
2019 (12)
2016 (11)
2015 (11)

Modelling Approach

Ordinary differential equation model (13)
Other (2)
Constraint-based model (2)

Lab affiliation

Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium (13)
Molecular Biosciences and the Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA (9)
Molecular Biosciences and the Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX USA (6)
Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria (3)
School of Integrative Plant Science Plant Biology Section, Cornell University (3)
Department of Plant Systems Biology, University of Hohenheim, 70599 Stuttgart, Germany (3)
VIB-UGent Center for Plant Systems Biology (3)
Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany (3)
(1) Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; (2) VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium. (2)
Prof. Dr. Martin von Bergen Head of Department of Molecular Systems Biology Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 1211 Martin.vonbergen@ufz.de, http://www.ufz.de/index.php?de=40881 (2)
University of Vienna, Department of Ecogenomics and Systems Biology (2)
(1) Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; (2) VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium. (2)
Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia. (2)
Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Spain (2)
Molecular Systems Biology (2)
lab (2)
Molecular Biosciences and the Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX, USA (2)
Head, Chair Plant Biotechnology Faculty of Biology University of Freiburg Schaenzlestrasse 1 D-79104 Freiburg Germany (2)
Dept. of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University (1)
Dept. Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia. (1)
PI. Associate Professor Department of Plant and Microbial Biology. UCB. (1)
Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany (1)
Molecular Systems Biology Department of Ecogenomics and Systems Biology University of Vienna Austria (1)
State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China (1)
MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States. (1)
Plant Systems Biology, Universitaet Hohenheim, Garbenstrasse 30 (1)
Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Oviedo, Spain. University Institute of Biotechnology of Asturias, University of Oviedo, Oviedo, Spain. (1)
Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran (1)
Norwegian University of Science and Technology (NTNU), Department of Biology, Functional Plant Biology Group, Norway (1)
UMR 1332 BFP, INRA, Univ Bordeaux, F33883 Villenave d’Ornon, France (1)

IsPrivate

False (20)

Model Flag

Non Kinetic (4)

Submitter Keywords

TransQST (1)
FROG (1)

Classification

fungi (2)
protozoa (1)
bacteria (1)

Study type

Transcription profiling by array (377)
RNA-seq of coding RNA (157)
ChIP-seq (25)
Unknown experiment type (23)
Comparative genomic hybridization by array (13)
RNA-seq of coding RNA from single cells (13)
RNA-seq of non coding RNA (13)
Other (11)
Transcription profiling by tiling array (7)
Methylation profiling by array (7)
Plant - High-throughput sequencing (4)
High-throughput sequencing (4)
Genotyping by array (4)
Bisulfite-seq (4)
ChIP-chip by tiling array (3)
DNA-seq (3)
Transcription profiling by SAGE (1)
MeDIP-seq (1)
Human - Single-cell sequencing (1)
Human - High-throughput sequencing (1)
Animal - High-throughput sequencing (1)
Proteomic profiling by mass spectrometer (1)
ChIP-chip by array (1)
Transcription profiling by RT-PCR (1)
MicroRNA profiling by high throughput sequencing (1)
Single nucleus RNA sequencing (1)
MicroRNA profiling by array (1)
Genotyping by high throughput sequencing (1)
Methylation profiling by high throughput sequencing (1)
RNA-seq of total RNA (1)

Release Date

2022 (827)
2025 (808)
2021 (733)
2020 (701)
2023 (651)
2024 (589)
2019 (534)
2018 (487)
2015 (478)
2017 (450)
2016 (439)
2014 (398)
2013 (336)
2012 (289)
2011 (236)
2010 (213)
2009 (118)
2008 (109)
2026 (108)
2007 (55)
2006 (46)
2005 (43)
2004 (24)
2002 (10)
2003 (7)
2001 (6)
1999 (4)
1998 (3)
1997 (2)

Previous page
1 / 941
You're on page 1
page 2
page 3
page 4
page 5
page ...
page 941
Next page

Sort by:

Relevance

Page size

The response of Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis

Drastic alteration in macronutrients causes large changes in gene expression in the photosynthetic unicellular alga Chlamydomonas reinhardtii. Preliminary data suggested that cells follow a biphasic response to this change hinging on the initiation of lipid accumulation, and we hypothesized that ...

2015-06-29 | MTBLS208 | MetaboLights

Metabolic Profiling of Escherichia coli-Based Cell-Free Expression Systems for Process Optimization

Biotechnology has transformed the production of various chemicals and pharmaceuticals due to its efficient and selective processes, but it is inherently limited by its use of live cells as 'biocatalysts.' Cell-free expression (CFE) systems, which use a protein lysate isolated from whole cells, have ...

2020-06-02 | MTBLS1079 | MetaboLights

Studies on the production of fungal polyketides in Aspergillus nidulans using systems biology tools

Using genetic engineering tools available for the model organism Aspergillus nidulans, we constructed two recombinant strains; one expressing the model polyketide Penicillium griseofulvum 6-methylsalicylic acid (6-MSA) polyketide synthase gene, and one expressing the 6-MSA gene and overexpressing th...

ORGANISM(S): Emericella nidulans

2009-02-27 | E-GEOD-12859 | biostudies-arrayexpress

Plant hosts modify belowground microbial community response to extreme drought

Drought stress negatively impacts microbial activity, but the magnitude of stress responses are likely dependent on a diversity of below ground interactions. Populus trichocarpa individuals and no plant bulk soils were exposed to extended drought (~0.03% gravimetric water content (GWC) after 12d)...

2020-06-19 | MTBLS1463 | MetaboLights

Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli

Investigation of whole genome gene expression level in E. coli K-12 MG1655 in glucose M9 minimal media with/without heatshock A six chip study using total RNA recovered from E. coli K-12 MG1655 grown up to OD600nm 0.6 (mid-exponential phase) in M9 minimal media supplemented with 0.2% glucose with/wi...

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

2013-06-20 | E-GEOD-42675 | biostudies-arrayexpress

Systems Biology approach to identify transcriptome reprogramming in Arabidopsis thaliana during insect and bacterial attack (Brevicoryne brassicae)

We have implemented an integrated Systems Biology approach to analyze overall transcriptomic reprogramming and systems level defense responses in the model plant Arabidopsis thaliana during an insect (Brevicoryne brassicae) and a bacterial (Pseudomonas syringae pv. tomato strain DC3000) attack. The ...

ORGANISM(S): Arabidopsis thaliana

2013-06-01 | E-GEOD-39245 | biostudies-arrayexpress

A systems biology view of responses to lignin biosynthesis perturbations in Arabidopsis

Inflorescence stems of 20 Arabidopsis thaliana mutants, each mutated in a single gene of the lignin biosynthetic pathway (PAL1 , PAL2, C4H, 4CL1, 4CL2, CCoAOMT1, CCR1, F5H1, COMT and CAD6, two mutant alleles each) were analyzed by microarrays.

ORGANISM(S): Arabidopsis thaliana

2012-09-20 | E-MTAB-1284 | biostudies-arrayexpress

Plant species richness promotes the decoupling of leaf and root defence traits while species-specific responses in physical and chemical defences are rare

The increased positive impact of plant diversity on ecosystem functioning over time is often attributed to the gradual accumulation of mutualists and dilution of antagonists in diverse plant communities. While increased plant diversity alters traits related to resource acquisition, it remains unc...

2025-02-13 | MTBLS8464 | MetaboLights

Creation of a Plant Metabolite Spectral Library for Untargeted and Targeted Metabolomics

Large-scale high throughput metabolomic technologies are indispensable components of systems biology in terms of discovering and defining the metabolite parts of the system. However, the lack of a plant metabolite spectral library limited the metabolite identification of plant metabolomics study. He...

ORGANISM(S): Arabidopsis Thaliana (ncbitaxon:3702)

2022-12-03 | MSV000090829 | MassIVE

Systems biology of interstitial lung diseases

This SuperSeries is composed of the following subset Series: GSE21369: Gene expression profiles of interstitial lung disease (ILD) patients GSE21394: MicroRNA expression profiles of interstitial lung disease (ILD) patients Refer to individual Series

ORGANISM(S): Homo sapiens

2011-04-19 | E-GEOD-21411 | biostudies-arrayexpress

Previous page
1 / 941
You're on page 1
page 2
page 3
page 4
page 5
page ...
page 941
Next page

Sort by:

Relevance

Page size

9405 Results

Show results for

Organisms

Organisms

Repository

Tissue

Disease

Technology Type

Instrument Platform

Publication Date

UNIPROT ID/AC

CHEBI ID

Metabolite Name

First Public Date

Modelling Approach

Lab affiliation

Tags

IsPrivate

Model Flag

Submitter Keywords

Classification

Study type

Release Date

OmicsDI is part of the ELIXIR infrastructure

Tweets