Nuclease - OmicsDI

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Transcriptomics (6109)
Unknown (4951)
Genomics (2241)
Proteomics (505)
Other (150)
Metabolomics (17)
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Organisms

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Arabidopsis thaliana (193)
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Escherichia coli str. K-12 substr. MG1655 (38)
Pseudomonas aeruginosa (36)
Apis mellifera (34)
Mycobacterium tuberculosis (32)
Rhizobium leguminosarum (30)
Rattus rattus (25)
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Yersinia pestis (22)
Gallus gallus (21)
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Pseudomonas aeruginosa PAO1 (18)
Burkholderia cenocepacia (16)
Vitis vinifera (15)

Organisms

Homo sapiens (414)
Mus musculus (230)
Saccharomyces cerevisiae (83)
Drosophila melanogaster (21)
Escherichia coli (16)
Arabidopsis thaliana (14)
Danio rerio (10)
Caenorhabditis elegans (9)
human viral metagenome (6)
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viral metagenome (6)
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synthetic construct (5)
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Escherichia coli BL21(DE3) (3)
human metagenome (3)
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1,4-dioxane-degrading enrichment culture (2)
Neisseria meningitidis 8013 (2)
Plasmodium falciparum 3D7 (2)
canine metagenome (2)
Clostridioides difficile (2)
human skin metagenome (2)

Repository

biostudies-arrayexpress (6533)
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geo (602)
pride (427)
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NODE (2)
PeptideAtlas (2)
ExpressionAtlas (1)
dbGaP (1)
EVA (1)

Tissue

Cell culture (115)
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Large cell carcinoma (1)
Invasive pituitary adenoma (1)
Oropharynx squamous-cell carcinoma in DiseaseLocation oropharynx has DiseaseStaging lymph node negative (N0) (1)
Hepatocellular carcinoma-non tumorous region (1)
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CUP (1)
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Subjective memory loss (1)
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EAE-resistant (1)
Myelogenous leukaemia (1)

Technology Type

Mass Spectrometry (427)
Shotgun proteomics (180)
Bottom-up proteomics (98)
Affinity purification coupled with mass spectrometry proteomics (74)
Data-dependent acquisition (50)
Data-independent acquisition (32)
Gel-based experiment (26)
Chemical cross-linking coupled with mass spectrometry proteomics (19)
SWATH MS (17)
Top-down proteomics (16)
Mass spectrometry (10)
Mass spectrometry (7)
P100 (7)
Mass spectrometry assay (7)
HDMSE (6)
RNA mass spectrometry (5)
SRM/MRM (5)
All-ion fragmentation (4)
Illumina HiSeq 2000 (3)
Immunopeptidomics (3)
MSE (3)
Illumina MiSeq (2)
Unknown, Affymetrix 500K (2)
Illumina HiSeq 2000, NextSeq 500, ILLUMINA (1)
ILLUMINA, Illumina HiSeq 2000 (1)
ISelect Beadchip (1)
Affymetrix 500K, unknown (1)
Illumina HumanExome-12v1_A-GenCall, zCall, GenoSNP, - Illuminus (1)
Illumina HiSeq 2000, ILLUMINA (1)
Illumina Genome Analyzer II (1)

Instrument Platform

Illumina NovaSeq 6000 (199)
NextSeq 500 (148)
Illumina HiSeq 2000 (129)
Illumina HiSeq 2500 (119)
Illumina HiSeq 4000 (87)
NextSeq 550 (45)
NextSeq 2000 (27)
Illumina MiSeq (23)
Axon GenePix 4000B scanning hardware (16)
Illumina NovaSeq X (13)
GenePix 4000B [Axon Instruments] (12)
Illumina HiSeq 3000 (12)
Illumina Genome Analyzer IIx (11)
Illumina HiSeq 1500 (11)
GenePix 4000A [Axon Instruments] (10)
Illumina Genome Analyzer II (10)
Scanning hardware (10)
DNBSEQ-G400 (10)
BGISEQ-500 (9)
ArrayWoRx Biochip Reader [Applied Precision] (8)
GenePix Personal 4100A [Axon Instruments] (8)
G2565BA DNA microarray scanner [Agilent] (8)
HiSeq X Ten (8)
Element AVITI (6)
MinION (6)
Axon- GenePix4000B (5)
NA (5)
Illumina HiSeq 1000 (5)
Agilent 2100 Bioanalyzer (4)
ScanArray 4000 [PerkinElmer] (4)

Publication Date

2013 (807)
2014 (774)
2015 (769)
2010 (761)
2012 (683)
2011 (596)
2016 (497)
2008 (285)
2023 (260)
2009 (238)
2025 (233)
2026 (216)
2024 (210)
2022 (210)
2021 (198)
2020 (172)
2019 (148)
2017 (145)
2018 (136)
2007 (121)
2005 (93)
2006 (81)
2004 (13)
2003 (6)
2002 (1)

UNIPROT ID/AC

A5A3E0 (2)
A6NHL2 (2)
A6NNZ2 (2)
B3KML9 (2)
B3KW93 (2)
B4DRV9 (2)
B4E3A4 (2)
B9VP19 (2)
D3DPU2 (2)
E7EVA0 (2)
E7EX29 (2)
E9PFP8 (2)
H0Y4R1 (2)
H0YM50 (2)
H7C144 (2)
I3L4N8 (2)
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K7EJH8 (2)
M0QY37 (2)
O00151 (2)
O14556 (2)
O14744 (2)
O14950 (2)
O14979 (2)
O15143 (2)
O15511 (2)
O43175 (2)
O43556 (2)
O43707 (2)
O43707-3 (2)

CHEBI ID

CHEBI:30831 (3)
CHEBI:17802 (3)
CHEBI:17754 (3)
CHEBI:17268 (3)
CHEBI:16704 (3)
CHEBI:17596 (3)
CHEBI:28681 (2)
CHEBI:60281 (2)
CHEBI:174173 (2)
CHEBI:76341 (2)
CHEBI:138529 (2)
CHEBI:143269 (2)
CHEBI:1606 (2)
CHEBI:28050 (2)
CHEBI:73018 (2)
CHEBI:86910 (2)
CHEBI:68434 (2)
CHEBI:87986 (2)
CHEBI:45441 (2)
CHEBI:17768 (2)
CHEBI:58148 (2)
CHEBI:82966 (2)
CHEBI:86543 (2)
CHEBI:73004 (2)
CHEBI:73008 (2)
CHEBI:73009 (2)
CHEBI:40521 (2)
CHEBI:70959 (2)
CHEBI:82965 (2)
CHEBI:50621 (2)

Metabolite Name

N1-Methyl-4-pyridone-3-carboxamide (2)
Pseudouridine (2)
Homocarnosine (2)
Adenosine (2)
N-acetyltryptophan (2)
Deoxyguanosine (2)
Guanosine (2)
Uridine (2)
N6-methyl-2’-deoxyadenosine (1)
Beryllium (1)
3-[(Cyanophenylmethyl)amino]-3-oxopropanoic acid (1)
Bitalin A 12-glucoside (1)
6-hydroxy-2-phenyl-4H-chromen-4-one (1)
2-Hydroxy-2-phenylacetonitrile O-[b-D-apiosyl-(1->2)-b-D-glucoside] (1)
7-Hydroxy-6-methoxy-alpha-pyrufuran (1)
5'-Methoxybilobetin (1)
Guanosine-monohosphate (1)
Adenosine 5'-Triphosphate (1)
Artomunoxanthentrione epoxide (1)
Erysothiopine (1)
Cytidine Triphosphate (1)
4,5-Dimethyl-2-heptyloxazole (1)
3-Mercapto-3-methyl-1-butanol (1)
Gamma-Glutamyl-S-methylcysteinyl-beta-alanine (1)
2-Aminoquinoline (1)
Jangomolide (1)
(7R*,8R*)-3-Methoxy-3',4,7,9,9'-pentahydroxy-8,4'-oxyneolignan 4-xyloside (1)
Irilone (1)
[8]-Gingerol (1)
5'-Cytidylic Acid (1)

First Public Date

2025 (181)
2023 (161)
2024 (146)
2026 (130)
2022 (122)
2019 (91)
2020 (87)
2021 (86)
2014 (78)
2017 (62)
2013 (55)
2018 (48)
2016 (48)
2015 (42)
2012 (3)
2010 (2)
2011 (1)

Classification

bacteria (42)
protozoa (8)
viruses (7)
fungi (3)
helminths (1)

Modification

N6 (1)
N6-dimethyl-L-lysine (1)
Not available (1)

Study type

Transcription profiling by array (3784)
RNA-seq of coding RNA (963)
ChIP-seq (516)
ChIP-chip by tiling array (127)
Other (108)
Comparative genomic hybridization by array (107)
RNA-seq of non coding RNA (106)
RNA-seq of coding RNA from single cells (94)
Transcription profiling by tiling array (80)
ChIP-chip by array (61)
Transcription profiling by RT-PCR (52)
Unknown experiment type (51)
RNA-seq of total RNA (49)
Methylation profiling by high throughput sequencing (42)
MicroRNA profiling by array (37)
ATAC-seq (34)
DNA-seq (33)
CUT&RUN (26)
Methylation profiling by array (24)
Animal - High-throughput sequencing (22)
Cell line - High-throughput sequencing (20)
MNase-seq (19)
High-throughput sequencing (19)
Genotyping by array (14)
RNAi profiling by array (12)
Human - High-throughput sequencing (10)
Hi-C (9)
CLIP-seq (7)
MicroRNA profiling by high throughput sequencing (7)
Single nucleus RNA sequencing (7)

Release Date

2015 (998)
2014 (985)
2013 (957)
2010 (834)
2012 (810)
2011 (723)
2016 (704)
2023 (515)
2022 (513)
2021 (513)
2020 (457)
2025 (418)
2024 (412)
2018 (410)
2017 (403)
2019 (392)
2008 (346)
2009 (334)
2007 (168)
2005 (138)
2026 (131)
2006 (128)
2004 (55)
2003 (35)
2002 (27)
2001 (22)
2000 (20)
1998 (13)
1999 (11)
1997 (4)

Lab affiliation

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States (5)
Functional Proteomics, ICR (5)
Centre for Cancer Cell & Molecular Biology Barts Cancer Institute Queen Mary University of London Charterhouse Square London EC1M 6BQ U.K. (3)
Institute of Cancer Research, London (3)
Medical Research Council Senior Research Fellow Associate Professor in RNA Biochemistry and Research Group Leader Centre for Synthetic and Systems Biology (SynthSys) University of Edinburgh Max Born Crescent CH Waddington Building, room 3.06 EH9 3BF Edinburgh UK (3)
Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd, La Jolla, CA 92037 (3)
NICM Health Research Institute, Western Sydney University (3)
University of Alabama at Birmingham, Department of Pathology, Division MCP, O'Neal Comprehensive Cancer Center (3)
Agricultural Biotechnology Research Center, Academia Sinica, Taiwan (2)
CNRS, University of Strasbourg, UMR7242, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg, France (2)
Caprion Biosciences Inc. (2)
Cell and Chemical Biology Leiden University Medical Center The Netherlands (2)
Centre for Proteome Research, Dept. Biochemistry & Systems Biology, University of Liverpool, Liverpool, UK (2)
Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin (2)
Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands (2)
Department of Chemistry and Biochemistry University of Bern Switzerland (2)
Department of Molecular Biology and Genetics, Lab of Proteome Research, Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119992, Russia (2)
Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency (2)
Harvard Medical School Cell Biology Department (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)
Institut Pasteur Unité des Interactions Bactéries-Cellules, Inserm U604, INRA USC2020 25 rue du Dr. Roux 75015 Paris France (2)
Lab of Proteome Research, Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia (2)
Max-Planck-Institute for Multidisciplinary Sciences Bioanalytical Mass Spectrometry Group Am Fassberg 11 D-37077 Goettingen, Germany University Medical Center Goettingen Bioanalytics Institute for Clinical Chemistry Robert Koch Strasse 40 D-37075 Goettingen, Germany (2)
Medical Oncology and Hematology, University Hospital and University of Zurich, Zurich, Switzerland (2)
NICM HRI, Western Sydney University, NSW, Australia (2)
Proteomics Center, Erasmus MC (2)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (2)
School of Life and Environmental Sciences, University of Sydney, NSW 2006 Australia (2)
The Walter and Eliza Hall Institute (2)
University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics (2)

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A Class 1 OLD family nuclease encoded by Vibrio cholerae is countered by a vibriophage-encoded direct inhibitor

Bacteria are constantly threatened by their viral predators (phages), which has resulted in the development of defense systems for bacterial survival. One family of defense systems found widely across bacteria are OLD (for overcoming lysogeny defect) family nucleases. Despite recent discoveries rega...

ORGANISM(S): Escherichia coli

2025-09-15 | PXD058617 | Pride

M-OM-^CB-dependent yabJ-spoVG operon involved in regulation of extracellular nuclease, lipase and protease expression in Staphylococcus aureus

The alternative sigma factor M-OM-^CB of Staphylococcus aureus is involved in the coordination of the general stress response, expression of virulence determinants and modulation of antibiotic resistance levels. It controls a large regulon, either directly by recognizing conserved M-OM-^CB promoter ...

ORGANISM(S): Staphylococcus aureus

2011-11-23 | E-GEOD-30115 | biostudies-arrayexpress

Off-Target Analysis of Zinc Finger Nucleases

Zinc Finger Nucleases (ZFNs) facilitate precise editing of DNA enabling targeted genomic modifications in vivo. ZFNs have been employed to obtain genetically modified plants and animals, and cell-based therapies utilizing ZFNs are undergoing clinical trials. However, many ZFNs display dose-dependent...

ORGANISM(S): Danio rerio

2010-08-25 | E-GEOD-23762 | biostudies-arrayexpress

Micrococcal nuclease sequencing analysis for nucleosome localization of mouse fetal liver erythroblasts

Nucleosomal DNA was prepared using Simple ChIP Enzymatic Chromatin IP Kit according to manufacturer’s instruction. Briefly, Nuclei were isolated from purified Ter119 negative or in vitro cultured erythroblasts. Cross-linked native chromatin was then digested with MNase into mononucleosomal DNA. Sequ...

ORGANISM(S): Mus musculus

2014-10-01 | E-GEOD-55825 | biostudies-arrayexpress

The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres

Plant and animal centromeres comprise megabases of highly repeated satellite sequences, yet centromere function can be specified epigenetically on single-copy DNA by the presence of nucleosomes containing a centromere-specific variant of histone H3 (cenH3). We determined the positions of cenH3 nucle...

ORGANISM(S): Oryza sativa

2013-11-06 | E-GEOD-50755 | biostudies-arrayexpress

Flap endonuclease 1 repairs DNA-protein crosslinks via ADP-ribosylation

The protein composition of DNA-protein crosslinks (DPCs) induced by formaldehyde treatment of human cell lines was analyzed by mass spectrometry.

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

2024-06-14 | MSV000095039 | MassIVE

MIF Nuclease Inhibition Protects CNS Neurons following Inflammation

PRJNA1187229 | ENA

A fluorogenic micrococcal nuclease-based probe for fast detection and optical imaging of Staphylococcus aureus in prosthetic joint and fracture-related infections.

Not available

S-EPMC11300479 | biostudies-literature

Nuclease-NTPase systems use shared molecular features to control bacterial anti-phage defense