Degradome - OmicsDI

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Genomics (553)
Unknown (508)
Transcriptomics (166)
Proteomics (59)
Other (39)
Methylation profiling (1)
Metabolomics (1)

Organisms

Oryza sativa (33)
Arabidopsis thaliana (28)
Homo sapiens (21)
Glycine max (15)
Solanum lycopersicum (14)
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Fragaria x ananassa (4)
Caenorhabditis elegans (4)
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Phalaenopsis aphrodite subsp. formosana (2)
Naumovozyma castellii (2)
Glycine soja (2)
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Solanum habrochaites (2)
Amborella trichopoda (2)
Populus euphratica (2)
Vanderwaltozyma polyspora (1)
Brassica juncea (1)

Organisms

Oryza sativa (31)
Arabidopsis thaliana (30)
Zea mays (13)
Solanum lycopersicum (12)
Glycine max (12)
Homo sapiens (9)
Camellia sinensis (8)
Brassica napus (7)
Prunus persica (6)
Arachis hypogaea (5)
Gossypium hirsutum (5)
Solanum tuberosum (5)
Triticum aestivum (5)
Vitis vinifera (5)
Mus musculus (5)
Triticum turgidum subsp. durum (4)
Populus x canadensis (4)
Hordeum vulgare (4)
Zea mays subsp. mays (4)
Oryza sativa Japonica Group (4)
Phaseolus vulgaris (4)
Betula luminifera (3)
Medicago ruthenica (3)
Quercus robur (3)
Panax notoginseng (3)
Rosa rugosa (3)
Ginkgo biloba (3)
Medicago sativa (3)
Cucumis sativus (3)
Penicillium italicum (2)

Repository

ENA (458)
geo (220)
biostudies-arrayexpress (81)
pride (51)
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Tissue

Cell culture (16)
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Articular cartilage (1)
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Disease

Systemic lupus erythematosus (2)
Acute leukemia (2)
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Chronic myeloid leukemia (1)
Osteoarthritis (1)
Malignant neoplasm of ovary (1)
Disease free (1)

Technology Type

Mass Spectrometry (51)
Shotgun proteomics (37)
Bottom-up proteomics (10)
Data-independent acquisition (4)
Data-dependent acquisition (4)
Affinity purification coupled with mass spectrometry proteomics (4)
Gel-based experiment (3)
Mass spectrometry (1)
SRM/MRM (1)

Instrument Platform

LTQ Orbitrap Elite (2)
Orbitrap Fusion Lumos (2)
Illumina HiSeq 2500 (1)
MaXis 4G (1)
Q Exactive Plus (1)
Liquid Chromatography MS - negative - reverse phase (1)
Liquid Chromatography MS - positive - reverse phase (1)
Thermo Scientific LTQ (1)
Thermo Scientific LTQ Orbitrap XL (1)
LTQ-Orbitrap (1)

Publication Date

2021 (35)
2016 (29)
2015 (29)
2020 (27)
2013 (26)
2012 (26)
2019 (24)
2018 (24)
2023 (22)
2014 (19)
2025 (18)
2017 (16)
2010 (15)
2024 (15)
2022 (14)
2011 (10)
2026 (6)
2009 (4)
2008 (1)

CHEBI ID

CHEBI:168226 (1)
CHEBI:189815 (1)
CHEBI:187390 (1)
CHEBI:185326 (1)
CHEBI:192966 (1)
CHEBI:192965 (1)
CHEBI:134608 (1)
CHEBI:74057 (1)
CHEBI:187414 (1)
CHEBI:186342 (1)
CHEBI:184458 (1)
CHEBI:184999 (1)
CHEBI:27648 (1)
CHEBI:191476 (1)
CHEBI:192964 (1)
CHEBI:165334 (1)
CHEBI:192963 (1)
CHEBI:183529 (1)
CHEBI:185673 (1)
CHEBI:191816 (1)
CHEBI:165484 (1)
CHEBI:192962 (1)
CHEBI:46734 (1)
CHEBI:192961 (1)
CHEBI:192960 (1)
CHEBI:168173 (1)
CHEBI:186825 (1)
CHEBI:187304 (1)
CHEBI:192959 (1)
CHEBI:191433 (1)

Metabolite Name

4-[5]-ladderane-butanoic acid (1)
Scutellarein 6,7,4'-trimethyl ether 5-(6'''-acetylglucosyl)(1->3)-galactoside (1)
4,4,14alpha-trimethyl-5alpha-cholest-9(11),24-dien-3beta-ol (1)
Ent-9-A1-PhytoP (1)
7,8-epoxy-17S-HDHA (1)
7,3',4'-Trihydroxy-5-methoxy-6-C-methylflavanone 7-O-glucoside (1)
3-Ketohexanoyl-CoA (1)
Quercetin 3-(2''-galloylgalactoside) (1)
PGE3 1,15-lactone (1)
Catechin 4'-O-beta-D-glucopyranoside (1)
3Z,13Z-octadecadien-1-ol (1)
Kenusanone D (1)
Transilitin (1)
6-{[2-({4,5-dihydroxy-6-methyl-2-[(3,4,5,6-tetrahydroxyoxan-2-yl)methoxy]oxan-3-yl}oxy)-3,5-dihydroxy-6-methyloxan-4-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid (1)
9,10-dihydroxy-13-hydroperoxy-11-octadecenoic acid (1)
R-nostrenol (1)
8,9-Epoxy-2Z-decene-4,6-diynoic acid (1)
Quercetin 3-gentiobioside-7-glucuronide (1)
Quercetin 4'-glucuronide (1)
Maritimetin 6-(6''-acetylglucoside) (1)
3,5,7,3',4'-Pentahydroxy-6-methoxyflavan 3-O-[glucopyranosyl-(4->1)-alpha-D-xylopyranoside] (1)
5,11-dodecadiynoic acid (1)
D17 PGE1 (1)
5,8,11-heptadecatriynoic acid (1)
Matteuorienate B (1)
4Z,8Z,11Z-Heptadecatriene (1)
Luteolin 7-(6''-malonylneohesperidoside) (1)
(22E)-(24R)-24,25-dihydroxy-22,23-didehydrovitamin D3 (1)
14-F2-dihomo-IsoP (1)
3Z,6E,8E-Dodecatrien-1-ol (1)

First Public Date

2024 (48)
2020 (48)
2021 (46)
2022 (38)
2025 (36)
2023 (36)
2017 (36)
2013 (35)
2018 (32)
2019 (29)
2016 (26)
2015 (22)
2026 (14)
2014 (12)

Classification

fungi (3)

Modification

15.994915 (2)
57.021464 (2)
6.020129 (1)
45.029395 (1)
10.008269 (1)
-17.026549 (1)
42.010565 (1)
4x(2)H labeled dimethylated L-lysine (1)
4x(15)N labeled L-arginine (1)
N6-dimethyl-L-lysine (1)
+3amu) (1)
Not available (1)

Study type

RNA-seq of non coding RNA (40)
RNA-seq of coding RNA (26)
Other (8)
Transcription profiling by array (7)

Release Date

2021 (58)
2016 (56)
2022 (47)
2020 (43)
2015 (39)
2013 (38)
2019 (38)
2014 (37)
2012 (36)
2017 (35)
2025 (35)
2023 (35)
2018 (33)
2024 (21)
2011 (15)
2010 (11)
2009 (4)
2026 (3)
2006 (2)
2008 (1)
2004 (1)
2003 (1)

Lab affiliation

Weizmann Institute of Science (7)
Technical University of Denmark (2)
DTU Bioengineering (2)
Institute of Molecular Medicine and Cell Research, University of Freiburg, Germany (1)
Center for Blood Research, Life Sciences Centre, University of British Columbia; Vancouver, British Columbia, Canada, V6T 1Z3. (1)
Center for Blood Research, Life Sciences Centre, University of British Columbia; Vancouver, British Columbia, Canada, V6T 1Z3 (1)
Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia (1)
Faculty of Biology, Technion - Israel Institute of Technology Haifa, Israel (1)
Wiezmann institude of science (1)
Laboratório Especial de Toxinologia Aplicada, Instituto Butantan,Av. Vital Brasil 1500, 05503-000, São Paulo, Brazil. (1)
German Cancer Research Center, Division Proteomics of Stem Cells and Cancer, Heidelberg, Germany Heidelberg University, Medical Faculty, Heidelberg, Germany (1)
Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada. (1)
University of Göttingen, Dept. of Evolutionary Developmental Genetics, Germany (1)
Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education; Warsaw, Poland Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology; Warsaw, Poland (1)
Department of Chemistry, Umeå University, Umeå, Sweden (1)
Department of Cell Biology, Harvard Medical School, Boston, MA 02115 USA (1)
Research Institute of Molecular Pathology – IMP, and Institute of Molecular Biotechnology – IMBA (1)
University of Kiel Institute of Biochemistry Unit for Degradomics of the Protease Web Otto-Hahn-Platz 9 24118 Kiel Germany (1)
Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK (1)
Environmental Molecular Sciences Laboratory (1)
Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, University of Kiel, Kiel, Germany (1)
Ghent University, VIB (1)
Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia (1)
Queensland University of Technology at the Translational Research Institute, Level 3 West, 37 Kent Strreet, Woolloongabba, QLD 4102 Australia (1)
Queensland University of Technology at the Translational Research Institute, Level 3 West, 37, Kent Street, Woolloongabba, QLD, 4102, Australia (1)
Faculty of Biology Technion-Israel Institute of Technology Haifa, Israel (1)
Laboratório de Toxinologia Aplicada Center of Toxins, Immune-Response and Cell Signaling (CeTICS) Instituto Butantan - Brazil (1)
Medical Protein Chemistry (1)
Faculty of Biology Technion - Israel Institute of Technology Haifa, Israel (1)
College of Life Sciences, Hunan Normal University (1)

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Identification of chilling stress-responsive tomato microRNAs and their target genes by high-throughput sequencing and degradome analysis

To identify tomato miRNAs involved in chilling response, two small RNA libraries and two degradome libraries from chilling-treated(4M-BM-0C/4M-BM-0C for 1hM-oM-

ORGANISM(S): Solanum habrochaites

2015-03-03 | E-GEOD-57335 | biostudies-arrayexpress

Identification of soybean seed developmental stage specific and tissue specific miRNA targets by degradome sequencing .

Five degradome libraries were constructed from three different seed developmental stages. Separate degradome libraries were constructed for seed coat and cotyledons to identify the tissue specific miRNAs and their potential targets. Sequencing and analysis of degradome libraries gives identification...

ORGANISM(S): Glycine max

2012-08-07 | E-GEOD-34433 | biostudies-arrayexpress

Genome-wide profiling of miRNAs and their target genes during somatic embryogenesis in cotton by small RNA and degradome sequencing

MicroRNAs (miRNAs) are endogenous non-coding ~21 nucleotide (nt) RNAs that regulate gene expression at transcriptional and post-transcriptional levels in plants and animals. They play an important role in development, abiotic stress responses or pathogen responses. miRNAs with their related target g...

ORGANISM(S): Gossypium hirsutum

2013-03-08 | E-GEOD-41132 | biostudies-arrayexpress

Degradome analysis in Phalaenopsis aphrodite subsp. formosana

We performed one degradome sequencing for identification and characterization of novel microRNAs in Phalaenopsis aphrodite subsp. formosana. Plant tissues of leaves, stalk, and flower buds frozen in liquid nitrogen were ground to fine powder using a mortar and pestle, respectively. Total RNA extract...

ORGANISM(S): Phalaenopsis aphrodite subsp. formosana

2012-11-06 | E-GEOD-35739 | biostudies-arrayexpress

Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, an...

ORGANISM(S): Oryza sativa Indica Group

2010-01-01 | E-GEOD-19050 | biostudies-arrayexpress

Degradome sequencing in Medicago truncatula roots (Glomus intraradices colonized and non-colonized)

Identification of microRNA targets in M. truncatula roots Degradome sequencing of mycorrhizal and non-mycorrhiza M. truncatula roots

ORGANISM(S): Medicago truncatula

2011-06-16 | E-GEOD-26217 | biostudies-arrayexpress

Degradome sequencing analysis in developing wheat grains

We aimed to identify targets of miRNAs during wheat grain development by using degradome sequencing approach. Two degradome libraries were constructed from wheat grains. Verification of miRNA targets from two degradome libraries in developing wheat grains.

ORGANISM(S): Triticum aestivum

2016-07-03 | E-GEOD-65798 | biostudies-arrayexpress

degradome sequence data

To identity the targets of miRNAs, we bundled 12 samples from different developing satages into four mixture samples. These samples were used to cosntruct degradome libraries and preform degradome sequencing on Illumina Hi-seq 2000 analyzer. More than 44.98 millions clean reads were obtained and 33....

ORGANISM(S): Glycine max

2017-05-01 | E-GEOD-72903 | biostudies-arrayexpress

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