Petri S S - OmicsDI

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Transcriptomics (807)
Unknown (704)
Proteomics (205)
Genomics (65)
Metabolomics (53)
Models (32)
Genomic (2)

Organisms

Homo sapiens (226)
Mus musculus (165)
Arabidopsis thaliana (153)
Danio rerio (47)
Saccharomyces cerevisiae (39)
Drosophila melanogaster (32)
Rattus norvegicus (32)
Caenorhabditis elegans (19)
Medicago truncatula (16)
Hordeum vulgare (13)
Paxillus involutus (8)
Solanum tuberosum (8)
Bacillus amyloliquefaciens (7)
Solanum lycopersicum (6)
Podospora anserina (5)
Neisseria meningitidis (5)
Vitis vinifera (5)
Hordeum vulgare subsp. vulgare (5)
Sus scrofa (5)
Tetranychus urticae (4)
Saccharina latissima (4)
Ectocarpus siliculosus (4)
Gerbera hybrid cultivar (4)
Lotus japonicus (4)
Populus tremula x Populus alba (4)
Bos taurus (4)
Oryza sativa Japonica Group (4)
Pseudomonas protegens (3)
Myxococcus xanthus (3)
Cucumis melo (3)

Organisms

Mus musculus (8)
Arabidopsis thaliana (5)
Streptomyces coelicolor (2)
Solanum nigrum (1)
Gossypium barbadense (1)
Entamoeba histolytica (1)
Synechocystis sp. PCC 6803 (1)
Pyricularia oryzae 70-15 (1)
Zea mays (1)
Oryza sativa Japonica Group (1)
Drosophila melanogaster (1)

Repository

biostudies-arrayexpress (844)
pride (178)
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geo (6)
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Disease

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ARR1-SRDX (1)
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Aortic valve stenosis (1)
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Brain glioma (1)
Cystic fibrosis (1)
Glioblastoma (1)
Heart failure (1)

Technology Type

Mass Spectrometry (178)
Shotgun proteomics (113)
Mass spectrometry (45)
Bottom-up proteomics (25)
Affinity purification coupled with mass spectrometry proteomics (22)
Data-dependent acquisition (14)
Data-independent acquisition (8)
Gel-based experiment (8)
SWATH MS (8)
Mass spectrometry assay (7)
Chemical cross-linking coupled with mass spectrometry proteomics (5)
HDMSE (5)
Top-down proteomics (2)
NMR spectroscopy (1)
DiaPASEF (1)
Immunopeptidomics (1)
Mass spectrometry imaging (1)

Instrument Platform

Illumina NovaSeq 6000 (45)
Illumina HiSeq 4000 (25)
Illumina HiSeq 2000 (17)
NextSeq 500 (17)
Illumina HiSeq 2500 (14)
Scanning hardware (8)
Illumina NovaSeq X (6)
ScanArray Express HT (5)
Illumina Genome Analyzer II (5)
Genepix (4)
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Agilent Scanner G2505B (2)
ScanArray 5000 [PerkinElmer] (2)
418 [Affymetrix] (2)
GenePix 4000B [Axon Instruments] (2)
Illumina HiSeq 1000 (2)
Illumina HiSeq 1500 (2)
NextSeq 550 (2)
Ubuntu Linux (1)
Windows pc (1)
Petri dish (1)
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Growth chamber, fridge (1)
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Leica CM3050 S (cryostat), Leica Microsystems (microscope) (1)
GeneChip Scanner 2500 (1)
Roche Nimblegen MS200 scanner (1)
Hybridization system 4 station (1)
G2505B scanner (Agilent) (1)

Publication Date

2014 (111)
2010 (98)
2016 (93)
2011 (81)
2013 (73)
2012 (61)
2015 (60)
2022 (54)
2023 (51)
2008 (51)
2009 (49)
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2024 (45)
2025 (38)
2019 (36)
2020 (34)
2007 (34)
2026 (32)
2018 (25)
2017 (22)
2006 (21)
2005 (14)
2004 (7)

UNIPROT ID/AC

A5A3E0 (22)
B4E3A4 (22)
E7EX29 (22)
H7BZ94 (22)
O14744 (1)
O14980 (1)
O95149 (1)
P08621 (1)
P09012 (1)
P09234 (1)
P14678 (1)
P43487 (1)
P52292 (1)
P52297 (1)
P52298 (1)
P60510 (1)
P62304 (1)
P62306 (1)
P62308 (1)
P62314 (1)
P62316 (1)
P62318 (1)
P62826 (1)
Q09161 (1)
Q14974 (1)
Q16637 (1)
Q8IZH2 (1)
Q92973 (1)
Q96RS0 (1)
Q9H814 (1)

ENSEMBL ID

ENSG00000170477 (16)
ENSG00000147251 (6)
ENSG00000247315 (5)
ENSG00000229353 (4)
ENSG00000204131 (1)

CHEBI ID

CHEBI:15428 (46)
CHEBI:15354 (39)
CHEBI:15422 (31)
CHEBI:11561 (30)
CHEBI:12071 (30)
CHEBI:12109 (30)
CHEBI:12266 (30)
CHEBI:12886 (30)
CHEBI:12936 (30)
CHEBI:13086 (30)
CHEBI:15343 (30)
CHEBI:15345 (30)
CHEBI:15346 (30)
CHEBI:15350 (30)
CHEBI:15351 (30)
CHEBI:15361 (30)
CHEBI:15377 (30)
CHEBI:15379 (30)
CHEBI:15380 (30)
CHEBI:15414 (30)
CHEBI:15440 (30)
CHEBI:15441 (30)
CHEBI:15442 (30)
CHEBI:15467 (30)
CHEBI:15468 (30)
CHEBI:1547 (30)
CHEBI:15504 (30)
CHEBI:15521 (30)
CHEBI:15525 (30)
CHEBI:15531 (30)

Metabolite Name

Glycine (9)
L-Valine (9)
Cytidine (8)
L-Phenylalanine (8)
Leucine (8)
Phenylalanine (8)
Alanine (7)
Citric acid (7)
Guanosine (7)
L-Tyrosine (7)
Proline (7)
Succinate (7)
Taurine (7)
Tyrosine (7)
Valine (7)
Adenine (6)
Asparagine (6)
Choline (6)
Fumarate (6)
Glucose (6)
Glutamine (6)
Glycine (6)
Guanine (6)
Hypoxanthine (6)
Isoleucine (6)
L-Leucine (6)
L-Tryptophan (6)
Lactate (6)
Nonanoic acid (6)
Ornithine (6)

First Public Date

2021 (9)
2014 (7)
2022 (3)
2019 (3)
2017 (3)
2024 (2)
2025 (1)
2023 (1)
2020 (1)
2018 (1)
2013 (1)

Modelling Approach

Ordinary differential equation model (1)
Petri net (1)

Lab affiliation

Associate Member Developmental Neurobiology St. Jude Children's Research Hospital (8)
DZNE Munich, Neuroproteomics, Feodor-Lynen Str. 17, 81377 Munich, Germany (4)
University of Alabama at Birmingham, Department of Pathology, Division MCP, O'Neal Comprehensive Cancer Center (4)
EDyP (3)
Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, Campos dos Goytacazes, RJ, Brazil. Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil. (3)
OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands (3)
Ruhr University Bochum, Medical Faculty, Medizinisches Proteom-Center (3)
Centre for Functional Ecology, University of Coimbra (2)
Department of Glycobiology, Institute of Chemistry, Slovak Academy of Sciences (2)
Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia Universidade Estadual do Norte Fluminense Darcy Ribeiro Av. Alberto Lamego 2000 Campos dos Goytacazes-RJ, Brazil 28013-602 (2)
Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V. (2)
MPIs for Brain Research and Biophysics (2)
Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany (2)
Mendel University in Brno (2)
1. Center for Medical Biotechnology, VIB, Ghent, Belgium 2. Department for Biomolecular Medicine, Ghent University, Ghent, Belgium 3. VIB Proteomics Core, VIB, Ghent, Belgium (1)
1. Research Institute of Resource Insects, Chinese Academy of Forestry (1)
AG Evolutionäre Genetik der Pflanzen Fak. V - Institut für Biologie und Umweltwissenschaften (IBU) Carl von Ossietzky Universität Oldenburg Carl von Ossietzky-Str. 9-11 26111 Oldenburg (1)
Affiliation: Division of Cell Matrix Biology & Regenerative Medicine, The University of Manchester [Data also submitted and owned by Dr Matiss Ozols (matiss.ozols@manchester.ac.uk)] (1)
Agronomy College, Henan Agricultural University, China (1)
Analytical Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy (1)
Assistant professor, Biochemistry and Molecular Biology, Johns Hopkin Bloomberg Schools of Public Health, USA. (1)
Associate Professor, Division of Hematology, Department of Internal Medicine, The Ohio State University Wexner Medical Center (1)
Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales Sydney, NSW 2052, Australia. Palaeontology, Geobiology and Earth Archives Research Centre, University of New South Wales Sydney, NSW 2052, Australia. (1)
Biological Mass Spectrometry Lab, Department of Translational Medicine (DiMeT), Center for Translational Research on Autoimmune & Allergic Diseases - CAAD University of Piemonte Orientale, Novara, Italy (1)
Bristol Dental School, University of Bristol (1)
Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada. (1)
Cellzome, a GSK company (1)
Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, 85748 Garching, Germany (1)
Centre de Recherche sur le Cancer de l‘Université Laval,Oncology, Centre de Recherche du CHU de Québec-Université Laval, Canada, G1R 3S3 (1)
City University of New York Advanced Science Research Center - Nanoscience Department, USA City University of New York Hunter College -Chemistry & Biochemistry Department, USA (1)

IsPrivate

False (32)

Model Flag

Non Kinetic (30)

Classification

protozoa (1)

Modification

4x(15)N labeled L-arginine (1)

Study type

Transcription profiling by array (550)
RNA-seq of coding RNA (152)
ChIP-seq (25)
RNA-seq of non coding RNA (16)
Transcription profiling by tiling array (15)
RNA-seq of coding RNA from single cells (14)
Animal - High-throughput sequencing (6)
RNA-seq of total RNA (6)
High-throughput sequencing (4)
Other (4)
DNA-seq (4)
Methylation profiling by array (4)
Unknown experiment type (3)
Comparative genomic hybridization by array (3)
Methylation profiling by high throughput sequencing (3)
Plant - High-throughput sequencing (2)
Plant - One-color microarray (2)
Cell line - High-throughput sequencing (2)
Transcription profiling by RT-PCR (2)
MicroRNA profiling by array (2)
Genotyping by high throughput sequencing (2)
Transcription profiling by array of Physcomitrella patens Reute development (1)
Animal - One-color microarray (1)
ChIP-chip by tiling array (1)
Human - Single-cell sequencing (1)
Cell line - One-color microarray (1)
Proteomic profiling by mass spectrometer (1)
RNAi profiling by array (1)
ChIP-chip by array (1)
CLIP-seq (1)

Release Date

2014 (105)
2010 (104)
2015 (102)
2022 (99)
2024 (97)
2011 (95)
2023 (91)
2013 (90)
2016 (83)
2021 (80)
2025 (78)
2012 (76)
2020 (74)
2009 (60)
2018 (57)
2008 (57)
2019 (53)
2017 (45)
2007 (38)
2006 (24)
2026 (15)
2005 (14)
2004 (8)
2003 (1)
2001 (1)

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A Numerical Comparison of Petri Net and Ordinary Differential Equation SIR Component Models.

Not available

S-EPMC11275704 | biostudies-literature

Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets

The investigation of spliceosomal processes is currently a topic of intense research in molecular biology. In the molecular mechanism of alternative splicing, a multi-protein–RNA complex – the spliceosome – plays a crucial role. To understand the biological processes of alternative splicing, it is e...

2024-10-31 | MODEL2410300001 | BioModels

Automatic construction of Petri net models for computational simulations of molecular interaction network.

Not available

S-EPMC11550427 | biostudies-literature

Excess S-Adenosylmethionine inhibits methylation via catabolism to adenine

PRJNA764914 | ENA

A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina

A genome wide microarray, covering the 10546 presently known and predicted CDS, has been constructed with the Agilent in-situ synthesized 60-mers technology. 1) A library of 10 oligonucleotides per CDS has been design by the manufacturer. 2) A computational step has been performed to determine 3' po...

ORGANISM(S): Podospora anserina

2010-06-30 | E-GEOD-20734 | biostudies-arrayexpress

Expression data from Medicago truncatula roots treated with S. meliloti wild-type or exoA mutant bacteria, or auxin transport inhibitors

Publication title: Pseudonodule formation by wild type and symbiotic mutant Medicago truncatula in response to auxin transport inhibitors This SuperSeries is composed of the following subset Series: GSE27991: Expression data of Medicago truncatula Jemalong A17 roots treated with auxin transport inh...

ORGANISM(S): Medicago truncatula

2011-03-25 | E-GEOD-28174 | biostudies-arrayexpress

Comparative genomics of Steinernema reveals deeply conserved regulatory networks in nematodes

Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode...

ORGANISM(S): Caenorhabditis elegans

2015-06-05 | E-GEOD-68588 | biostudies-arrayexpress

TFPIα anticoagulant function is highly dependent on protein S in vivo.

Not available

S-EPMC11809661 | biostudies-literature

Transcription profiling of Medicago truncatula germinated seedlings grown in Petri dishes for 3 days then carry out salt stress

time-course salt stress experiment of model legume Medicago truncatula roots using Affymetrix Medicago Array, aimed to dig some useful gene for improve salt resistance for legumes and other crops Experiment Overall Design: 4 samples of Medicago truncatula germinated seedlings Experiment Overall Desi...

ORGANISM(S): Medicago truncatula

2009-12-03 | E-GEOD-13921 | biostudies-arrayexpress

Laminin G1 residues of protein S mediate its TFPI cofactor function and are competitively regulated by C4BP.

Not available

S-EPMC8791571 | biostudies-literature

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