Eukaryotes - OmicsDI

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Unknown (13724)
Genomics (3107)
Transcriptomics (1202)
Proteomics (628)
Other (201)
Methylation profiling (71)
Models (26)
Metabolomics (16)
Multiomics (2)

Organisms

Arabidopsis thaliana (362)
Homo sapiens (343)
Saccharomyces cerevisiae (266)
Mus musculus (198)
Schizosaccharomyces pombe (99)
Drosophila melanogaster (97)
Caenorhabditis elegans (49)
Oryza sativa (34)
Escherichia coli (34)
Chlamydomonas reinhardtii (24)
Candida albicans (22)
Toxoplasma gondii (21)
Plasmodium falciparum (21)
Neurospora crassa (21)
Zea mays (20)
Danio rerio (16)
Gallus gallus (15)
Halobacterium salinarum (13)
Trypanosoma brucei (12)
Oryza sativa Japonica Group (11)
Saccharomyces cerevisiae SK1 (10)
Escherichia coli K-12 (9)
Yarrowia lipolytica (7)
Bos taurus (5)
Eukaryota (2)
Haematobia irritans (2)
Ostreococcus tauri (2)
Zea mays subsp. mays (2)
Sorghum bicolor (2)
unclassified eukaryotes (1)

Organisms

Arabidopsis thaliana (230)
Homo sapiens (216)
Saccharomyces cerevisiae (164)
Mus musculus (132)
Drosophila melanogaster (57)
Schizosaccharomyces pombe (52)
marine metagenome (38)
Caenorhabditis elegans (24)
Oryza sativa (23)
soil metagenome (23)
Escherichia coli (16)
Plasmodium falciparum (16)
Neurospora crassa (15)
Toxoplasma gondii (15)
Chlamydomonas reinhardtii (14)
seawater metagenome (13)
synthetic construct (12)
Danio rerio (12)
freshwater metagenome (11)
Candida albicans (11)
Tetrahymena thermophila (10)
Dictyostelium discoideum (8)
Zea mays (8)
Gallus gallus (7)
Trypanosoma brucei brucei (6)
Nicotiana tabacum (6)
Eukaryota (6)
sediment metagenome (6)
Bombyx mori (6)
marine sediment metagenome (6)

Repository

ENA (2606)
geo (1350)
biostudies-arrayexpress (620)
pride (507)
jPOST (40)
iProX (38)
MassIVE (32)
BioModels (25)
MetaboLights (15)
GPMDB (6)
PeptideAtlas (5)
PanoramaPublic (4)
Cell Collective (1)
GNPS (1)
NODE (1)
PAXDB (1)

Tissue

Cell culture (68)
Permanent cell line cell (25)
Leaf (22)
Plant cell (20)
Whole body (16)
Cell suspension culture (13)
Embryo (8)
Fibroblast (7)
Seedling (7)
Brain (6)
Epithelial cell (6)
Blood (5)
Embryonic stem cell (5)
Photosynthetic cell (5)
Prokaryotic cell (5)
Colon (4)
Flower (4)
Rosette (4)
Testis (4)
Cell line cell (3)
Ciliary body (3)
HeLa cell (3)
Heart (3)
Kidney (3)
Liver (3)
Primary cell (3)
Root (3)
Blood cell (2)
Early embryonic cell (2)
Marrow (1)

Disease

Disease free (11)
Malaria (9)
Not Available (6)
Toxoplasmosis (6)
Chagas disease (5)
Trypanosomiasis (5)
Plasmodium falciparum malaria (4)
Chronic myeloid leukemia (3)
Giardiasis (3)
Acute leukemia (2)
Colon cancer (2)
Frozen shoulder (2)
Normal (1)
Aspergillosis (1)
Brain cancer (1)
Cervix carcinoma (1)
Hyperhomocysteinemia (1)
Hypomyelinating leukodystrophy 7 with or without oligodontia and-or hypogonadotropic hypogonadism (1)
Kidney cancer (1)
Leishmaniasis (1)
Leukemia (1)
Male infertility (1)
Microsporidiosis (1)
Myopathy (1)
Neuroblastoma (1)
Osteoarthritis (1)
Trichomoniasis (1)
Trichothiodystrophy (1)
Tuberculosis (1)
Tuberous sclerosis (1)

Technology Type

Mass Spectrometry (507)
Shotgun proteomics (269)
Affinity purification coupled with mass spectrometry proteomics (111)
Bottom-up proteomics (88)
Data-dependent acquisition (55)
Gel-based experiment (40)
Chemical cross-linking coupled with mass spectrometry proteomics (25)
Mass spectrometry (10)
Top-down proteomics (9)
Data-independent acquisition (8)
SWATH MS (7)
HDMSE (6)
SRM/MRM (6)
Mass spectrometry assay (5)
Affinity proteomics (4)
All-ion fragmentation (2)
MSE (2)
Proteogenomics (2)
DiaPASEF (1)
Mass spectrometry imaging (1)

Instrument Platform

Illumina HiSeq 2000 (26)
Illumina HiSeq 2500 (5)
NextSeq 500 (4)
Illumina Genome Analyzer IIx (3)
Illumina NovaSeq 6000 (3)
RiboZero (2)
Trizol (Invitrogen); FastPrep (MP Biochemicals) (2)
DASGIP bioreactors (2)
AB SOLiD 4 System (2)
Axon GenePix 4000B scanning hardware (2)
Ion Torrent Proton (2)
Illumina MiSeq (2)
Illumina TruSeq Stranded Total RNA kit, Biomek FxP (Beckman Coulter) (1)
Agilent Bioanalyzer 2100 system (Agilent Technologies, California, USA) (1)
Agilent 2100 Bioanaylze (1)
RNeasy Plant Mini Kit & TURBOTM DNase (Ambion) (1)
ERCC Spike-in Kit (Ambion) & Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant kit (1)
Axon GenePix 4000A scanning hardware (1)
Illumina HiSEq 2500 (1)
GenePix 4000A [Axon Instruments] (1)
DNA Microarray Scanner BA [Agilent Technologies] (1)
Axon- GenePix4000B (1)
418 [Affymetrix] (1)
ScanArray Express HT [PerkinElmer] (1)
GenePix 4000B [Axon Instruments] (1)
Illumina Genome Analyzer II (1)
Scanning hardware (1)
Illumina HiSeq X (1)
Curie computer cluster (1)
Illumina HiSeq 1000 (1)

Publication Date

2024 (238)
2023 (223)
2025 (221)
2026 (159)
2011 (156)
2020 (152)
2021 (144)
2015 (141)
2022 (141)
2016 (131)
2019 (122)
2014 (116)
2013 (112)
2018 (106)
2010 (106)
2012 (90)
2017 (80)
2008 (55)
2009 (50)
2007 (38)
2006 (29)
2005 (20)
2004 (5)

UNIPROT ID/AC

P04821 (2)
P32485 (2)
P23900 (2)
P18851 (2)
P18852 (2)
P01149 (2)
P0CI39 (2)
P30291 (2)
P40957 (1)
P24871 (1)
Q06598 (1)
P24870 (1)
Q9CQJ7 (1)
P11440 (1)
P32581 (1)
P21190 (1)
P53438 (1)
P39001 (1)
P38615 (1)
P40073 (1)
P40048 (1)
P30304 (1)
Q9TW49 (1)
Q9VMS4 (1)
Q59E16 (1)
P08018 (1)
O61734 (1)
P00546 (1)
P20437 (1)
P32943 (1)

CHEBI ID

CHEBI:16856 (4)
CHEBI:18012 (4)
CHEBI:17754 (3)
CHEBI:15356 (3)
CHEBI:18186 (3)
CHEBI:16708 (3)
CHEBI:25017 (3)
CHEBI:16610 (3)
CHEBI:28044 (3)
CHEBI:15721 (3)
CHEBI:6650 (3)
CHEBI:15741 (3)
CHEBI:7916 (3)
CHEBI:16015 (3)
CHEBI:15428 (3)
CHEBI:30915 (3)
CHEBI:16027 (3)
CHEBI:16680 (3)
CHEBI:36080 (2)
CHEBI:15996 (2)
CHEBI:17552 (2)
CHEBI:32650 (2)
CHEBI:16189 (2)
CHEBI:86468 (2)
CHEBI:18095 (2)
CHEBI:17256 (2)
CHEBI:22605 (2)
CHEBI:45658 (2)
CHEBI:29242 (1)
CHEBI:33699 (1)

Metabolite Name

Tryptophan (3)
Serine (3)
Lysine (3)
Cysteine (3)
Cystathionine (3)
Arginine (3)
Adenine (3)
Histidine (3)
Phenylalanine (3)
Tyrosine (3)
Threonine (3)
Glutamine (3)
Alanine (3)
Valine (3)
Isoleucine (3)
Leucine (3)
Glycine (3)
S-adenosylmethionine (2)
Arabitol (2)
Sedoheptulose-7-phosphate (2)
Homoserine (2)
Pantothenic acid (2)
Glutamic acid (2)
Xylitol (2)
Pyridoxal (2)
Phenylpyruvate (2)
N-formylmethionine (2)
N-acetylalanine (2)
Indolelactate (2)
4-hydroxyphenylpyruvate (2)

First Public Date

2024 (306)
2025 (268)
2023 (255)
2019 (208)
2026 (204)
2014 (204)
2013 (185)
2022 (169)
2020 (168)
2021 (167)
2017 (128)
2018 (127)
2016 (112)
2015 (98)
2012 (7)

Modelling Approach

Ordinary differential equation model (10)
Metabolic network (3)
Mathematical model (2)
Differential equation model (2)
Delayed differential equation model (2)
Constraint-based model (1)

Lab affiliation

Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg im Breisgau, Germany (6)
Associate Professor, Department of Biology, Massachusetts Institute of Technology and Whitehead Institute of Biomedical Research (5)
Harvard Medical School (5)
EDyP (4)
Experimental Neurology, University Hospital, Frankfurt am Main, Germany (4)
Protein Biogenesis Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT (4)
Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA (3)
Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland (3)
Génétique Quantitative et Évolution - Le Moulon INRA - Univ. Paris Sud - CNRS - AgroParisTech Ferme du Moulon 91190 Gif-sur-Yvette, France (3)
LPHI, Univ Montpellier, CNRS, INSERM, Montpellier, France (3)
Plant Physiology Group Westfälische WIlhelms-Universität Münster Germany (3)
Proteomics & Metabolomics Facility, Center for Open Research Resources & Equipment University of Connecticut Storrs, CT 06269 (3)
Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic (3)
University of Edinburgh (3)
Babraham Institute (2)
Basic Immune System of Plants / Protein Mass Spectrometry Max Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10, 50829 Cologne, Germany (2)
CRG, UPF (2)
Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland (2)
Department of Cell Biology Harvard Medical School Boston, MA 02115 (2)
Department of Chemistry, Imperial College London, Molecular Research Science Hub, 80 Wood Lane, London W12 0BZ, United Kingdom. The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom. (2)
Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA (2)
Dept. of Biochemistry & Molecular Biology, Complex Carbohydrate Research Center, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, Dept. of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104 USA (2)
Genome Regulation, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland (2)
Head Proteomics Group, Leiden University Medical Center, Center for Proteomics and Metabolomics, PO Box 9600, Postal zone P1-Q, 2300 RC Leiden, The Netherlands (2)
Institute of Molecular Biosciences, University of Graz, Graz, 8010, Austria (2)
Institute of Parasitology Biology Center, Czech Academy of Sciences Branišovská 31 370 05 České Budějovice CZECH REPUBLIC (2)
Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences (2)
Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA (2)
Laboratory of Enzymology and Molecular Biology (LEBIMO), Institute of Biology, University of Campinas (UNICAMP) (2)
Laboratório de Biologia Molecular e Sistêmica de Tripanossomatídeos, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Parana, Brazil (2)

IsPrivate

False (25)

Model Flag

Non Kinetic (4)

Classification

protozoa (80)
fungi (44)
bacteria (38)
viruses (3)
helminths (2)

Modification

+3amu) (3)
N6 (3)
10.008269 (2)
15.994915 (2)
42.010565 (2)
45.029395 (2)
4x(15)N labeled L-arginine (2)
58.005479 (2)
N6-dimethyl-L-lysine (2)
-17.026549 (1)
3x(2)H labeled N6-acetyl-L-lysine (1)
4-tetrahydrothiazine-3-carboxylic acid (1)
Not available (1)

Study type

Transcription profiling by array (199)
RNA-seq of coding RNA (115)
RNA-seq of non coding RNA (78)
ChIP-seq (51)
ChIP-chip by tiling array (50)
Other (37)
ChIP-chip by array (21)
Methylation profiling by high throughput sequencing (17)
Transcription profiling by tiling array (13)
Unknown experiment type (10)
RNAi profiling by array (6)
Comparative genomic hybridization by array (5)
DNA-seq (3)
Methylation profiling by array (3)
RIP-seq (2)
RNA-seq of total RNA (2)
Transcription profiling by MPSS (1)
RIP-chip by array (1)
Plant - High-throughput sequencing (1)
Translation profiling (1)
High-throughput sequencing (1)
Genotyping by array (1)
Hi-C (1)

Release Date

2021 (1007)
2022 (969)
2023 (883)
2020 (880)
2019 (834)
2024 (816)
2025 (787)
2018 (766)
2015 (733)
2016 (722)
2014 (721)
2017 (715)
2013 (632)
2011 (602)
2012 (578)
2010 (517)
2009 (404)
2008 (389)
2007 (265)
2006 (258)
2005 (193)
2004 (124)
2003 (118)
2026 (89)
2002 (87)
2001 (73)
2000 (68)
1999 (43)
1998 (34)
1997 (23)

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Diversity in DNA: Identification of methylated deoxyadenosines in higher eukaryotes

Since the discovery that cytosine deoxynucleotides could be methylated (dC5m), not much is known in higher eukaryotes about modifications affecting other deoxynucleotides. Here, we now report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including ...

2015-11-16 | MTBLS276 | MetaboLights

Sediment eukaryotes

Sediment eukaryotes Raw sequence reads

PRJNA1133151 | ENA

Soil eukaryotes in Australia

PRJNA891465 | ENA

Eukaryotes associated with seagrass sediment

Raw sequence reads of eukaryotes associated with seagrass sediment

PRJNA597113 | ENA

Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes

Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG met...

ORGANISM(S): Fragilariopsis cylindrus

2014-03-13 | E-GEOD-46692 | biostudies-arrayexpress

unicellular eukaryotes and helminths

Unicellular eukaryotes and helminths Targeted loci environmental

PRJNA495046 | ENA

Bloom and post-bloom planktonic Eukaryotes

Bloom and post-bloom planktonic Eukaryotes Targeted loci environmental

PRJNA1117659 | ENA

Unicellular eukaryotes from Aegean Sea coastal waters

Unicellular eukaryotes from Aegean Sea coastal waters Raw sequence reads

PRJNA515026 | ENA

Microbial Eukaryotes of Croatian Hot springs