Dna viruses - OmicsDI

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Unknown (7227)
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Homo sapiens (145)
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human gammaherpesvirus 4 (14)
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marine metagenome (8)
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human metagenome (4)
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synthetic construct (4)
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human skin metagenome (3)
hot springs metagenome (3)
seawater metagenome (3)
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soil metagenome (3)

Repository

biostudies-arrayexpress (2301)
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geo (224)
pride (84)
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Tissue

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Myasthenia gravis (seropositive patient with low thymic hyperplasia) (1)
12 DAI with PepMV-EU isolate (1)
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Wolbachia infected (1)
Metastatic prostate cancer (1)
Mock 24 h (1)
Infected with Influenza A/WSN/33 (H1N1) (1)
Xenografts with H1299 cell line (1)
AIDS-KS, HIV+, nodular (late) stage (1)
Mock infected (1)
PMV infected (1)
Infected (1)
Simian immunodeficiency virus (1)

Technology Type

Mass Spectrometry (84)
Shotgun proteomics (51)
Mass spectrometry (14)
Bottom-up proteomics (13)
Affinity purification coupled with mass spectrometry proteomics (12)
Data-dependent acquisition (9)
Gel-based experiment (6)
Mass spectrometry assay (5)
Illumina HiSeq 2000 (4)
Top-down proteomics (4)
Chemical cross-linking coupled with mass spectrometry proteomics (3)
ILLUMINA, Illumina HiSeq 2000 (2)
Data-independent acquisition (2)
SWATH MS (2)
Illumina MiSeq, HiSeq X Ten, NextSeq 500, Illumina HiSeq 4000, Illumina HiSeq 2500, ILLUMINA (1)
NextSeq 500, Illumina HiSeq 2500, ILLUMINA (1)
Illumina HiSeq 2500, ILLUMINA (1)
ILLUMINA, Illumina MiSeq (1)
Illumina Genome Analyzer IIx, Illumina HiSeq 2000 (1)
Illumina HiSeq 2000, Illumina Genome Analyzer IIx (1)
Illumina HiSeq 2500 (1)
Illumina Genome Analyzer IIx (1)
Illumina HiSeq 2000, ILLUMINA (1)
NMR spectroscopy (1)
All-ion fragmentation (1)

Instrument Platform

Illumina NovaSeq 6000 (78)
NextSeq 500 (67)
Illumina HiSeq 2500 (34)
Illumina HiSeq 2000 (31)
Illumina HiSeq 4000 (22)
Illumina HiSeq 1500 (21)
Illumina MiSeq (16)
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Illumina NovaSeq X (8)
NextSeq 2000 (8)
Illumina Genome Analyzer IIx (7)
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PromethION (4)
Illumina Genome Analyzer II (4)
DNBSEQ-T7 (4)
G2565AA DNA microarray scanner [Agilent] (3)
NA (3)
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Bio-Rad T100 Thermocycler (2)
MA900, Sony (2)
10x Chromium Controller (2)
Sequel (2)
ScanArray 5000 [PerkinElmer] (2)
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Scanning hardware (2)
Illumina HiSeq X (2)
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Publication Date

2013 (301)
2012 (280)
2015 (269)
2014 (261)
2010 (207)
2011 (193)
2016 (159)
2008 (130)
2025 (115)
2009 (84)
2022 (83)
2023 (82)
2024 (77)
2021 (77)
2020 (71)
2026 (70)
2007 (62)
2019 (49)
2018 (41)
2017 (39)
2005 (25)
2006 (14)
2004 (8)
2003 (1)

CHEBI ID

CHEBI:16704 (5)
CHEBI:16750 (4)
CHEBI:16335 (4)
CHEBI:16040 (3)
CHEBI:16449 (3)
CHEBI:17596 (3)
CHEBI:229469 (2)
CHEBI:20129 (2)
CHEBI:19228 (2)
CHEBI:20794 (2)
CHEBI:19227 (2)
CHEBI:17822 (2)
CHEBI:17126 (2)
CHEBI:18186 (2)
CHEBI:28300 (2)
CHEBI:20607 (2)
CHEBI:17802 (2)
CHEBI:17562 (2)
CHEBI:28044 (2)
CHEBI:21891 (2)
CHEBI:27266 (2)
CHEBI:57589 (2)
CHEBI:16020 (2)
CHEBI:138900 (1)
CHEBI:136341 (1)
CHEBI:134642 (1)
CHEBI:229635 (1)
CHEBI:140366 (1)
CHEBI:28742 (1)
CHEBI:29083 (1)

Metabolite Name

Guanosine (3)
Phenylalanine (3)
2'-O-methyluridine (2)
7-methylguanosine (2)
2'-O-methylcytidine (2)
Uridine (2)
Inosine (2)
Cytidine (2)
Adenosine (2)
1-methyladenosine (2)
Valine (2)
N6-methyladenosine (2)
Taurine (2)
Serine (2)
Adenosine (2)
Cytosine (2)
Proline (2)
Isoleucine (2)
Guanosine (2)
5-carboxymethyluridine (1)
8-oxoguanosine (1)
5-methyl-2'-O-methyluridine (1)
4-(4-hydroxyphenyl)sulfonylphenol (1)
NAD⁺ (1)
Glu-glu (1)
Dihydrouridine (1)
TG(18:1/22:6/22:6) (1)
N6-,O2'dimethyladenosine (1)
N4-Methylcytidine (1)
HexCer(d32:1) (1)

First Public Date

2025 (133)
2024 (117)
2023 (93)
2013 (92)
2026 (86)
2019 (70)
2022 (69)
2020 (61)
2014 (60)
2018 (58)
2021 (57)
2017 (44)
2016 (31)
2015 (27)
2012 (5)
2011 (1)

Classification

viruses (228)
bacteria (10)
protozoa (1)

Modification

Not available (1)

Study type

Transcription profiling by array (1436)
RNA-seq of coding RNA (284)
RNA-seq of non coding RNA (80)
ChIP-seq (76)
Other (50)
RNA-seq of coding RNA from single cells (48)
Methylation profiling by array (35)
Unknown experiment type (32)
DNA-seq (29)
Comparative genomic hybridization by array (27)
Cell line - High-throughput sequencing (25)
RNA-seq of total RNA (22)
Transcription profiling by RT-PCR (21)
ChIP-chip by tiling array (15)
Genotyping by array (15)
Methylation profiling by high throughput sequencing (12)
Ribo-seq (10)
MicroRNA profiling by high throughput sequencing (8)
Genotyping by high throughput sequencing (7)
Transcription profiling by tiling array (6)
RNAi profiling by array (6)
One-color microarray (4)
Human - High-throughput sequencing (4)
Human - One-color microarray (4)
ChIP-chip by array (4)
ATAC-seq (4)
MicroRNA profiling by array (4)
Transcription profiling by SAGE (3)
High-throughput sequencing (3)
Animal - High-throughput sequencing (3)

Release Date

2022 (783)
2021 (750)
2023 (692)
2020 (606)
2015 (575)
2014 (545)
2025 (527)
2013 (527)
2024 (517)
2019 (467)
2012 (462)
2016 (451)
2018 (448)
2017 (388)
2011 (378)
2010 (363)
2008 (229)
2009 (192)
2007 (131)
2005 (89)
2026 (86)
2006 (73)
2003 (54)
2004 (49)
2002 (33)
2001 (32)
2000 (32)
1998 (26)
1999 (19)
1997 (3)

Lab affiliation

EDyP (5)
Department of Molecular Biology, Princeton University, USA (2)
State Key Laboratory of Oncology in South China (2)
1. Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom. 2. Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany. (1)
Ascano Lab, Biochemistry Department, Vanderbilt University, Nashville TN, USA (1)
Assistant Professor Biomedical and Pharmaceutical Sciences Department, ChapmanUniversity School of Pharmacy, Irvine,California, USA (1)
Associate Professor, Department of Biochemistry & Molecular Biology, UTMB Mass Spectrometry Director, University of Texas Medical Branch – Galveston, Texas, USA (1)
Biochemistry and Molecular Biology, Munger Lab, University of Rochester, USA (1)
Biotechnology and Bioengineering Center, Deptartment of Microbiology, Medical College of Wisconsin (1)
Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK (1)
Cell Biology Department, Harvard Medical School (1)
Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea (1)
Centre de Recherche du CHU Ste-Justine (1)
Centre to Impact AMR, Monash University; Clayton, 3800, Australia Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University; Clayton, 3800, Australia (1)
Chulalongkorn University Systems Bilogy center, Research affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand (1)
Department of Biochemistry and Biophysics Smilow Center for Translational Research Perelman School of Medicine University of Pennsylvania 3400 Civic Center Blvd Philadelphia, PA 19104 (1)
Department of Biochemistry and Biophysics Smilow Center for Translational Research Perelman School of Medicine University of Pennsylvania Room 9-124 (office) 3400 Civic Center Blvd Philadelphia, PA 19104 215-573-9423 (office) (1)
Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, US (1)
Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland. (1)
Department of Chemistry and Biochemistry Montana State University (1)
Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim, Norway Proteomics and Modomics Experimental Core Facility (PROMEC) at Norwegian University of Science and Technology, Trondheim, Norway (1)
Department of Environmental Toxicology, University of California, Davis, USA (1)
Department of Microbiology Icahn School of Medicine at Mount Sinai (1)
Department of Microbiology; Icahn School of Medicine at Mount Sinai; New York, NY, 10029; USA (1)
Department of Molecular Biology, Cristea Lab, Princeton University, USA (1)
Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA Livestrong Cancer Institutes and Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA (1)
Department of Pathology and Laboratory Medicine,University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA Division of Cancer Pathobiology,Children's Hospital of Philadelphia, Philadelphia, PA USA (1)
Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany (1)
Deptartment of Cellular and Molecular Pharmacology, School of Medicine, University of California San Francisco (UCSF), USA (1)
Faculty of Natural Sciences, Keele University, UK (1)

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Virus-encoded glycosyltransferases hypermodify DNA with diverse glycans

Enzymatic modification of DNA nucleobases can coordinate gene expression, nuclease protection or mutagenesis. We recently discovered a clade of phage-specific cytosine methyltransferase (MT) and 5-methylpyrimidine dioxygenase (5mYOX) enzymes that produce 5-hydroxymethylcytosine (5hmC) as a precur...

2024-08-22 | MTBLS10724 | MetaboLights

Moisture Modulates Soil Reservoirs of Active DNA and RNA viruses

Global proteomics analyses to identify viral proteins in the soil microbiome. Samples were digested with trypsin, then analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline.

ORGANISM(S): Environmental Samples <bacteria> (ncbitaxon:48479)

MSV000086144 | MassIVE

unclassified DNA viruses

Characterization of Amoeba viruses

PRJDB16175 | ENA

Detection of Human Viruses from wastewater sewage extracts

Sewage samples were collected and concentrated for Human and animal viruses. Viruses were cultured on Buffalo Green Monkey Cells (BGMK) and their genomic DNA/RNA were extracted and labeled with Cy3 and Cy5 respectively. Labeled DNA/RNA were hybridized unto the array and signals generated were analyz...

ORGANISM(S): Viruses

2008-04-18 | E-GEOD-11195 | biostudies-arrayexpress

Acute lung injury results from innate sensing of viruses by an ER stress pathway

Incursions of new pathogenic viruses into humans from animal reservoirs are occurring with alarming frequency. The molecular underpinnings of immune recognition, host responses, and pathogenesis in this setting arepoorly understood. We studied pandemic influenza viruses to determine the mechanism by...

ORGANISM(S): Mus musculus

2015-07-06 | E-GEOD-65075 | biostudies-arrayexpress

Viruses

Viruses overview

PRJNA202319 | ENA

Novel viruses naturally infecting Caenorhabditis nematodes trigger a small RNA response

C. elegans has served as a laboratory model organism due to its ease of manipulation and the availability of both forward and reverse genetics. In recent years, efforts to study host-pathogen interactions in C. elegans have increased. For example, analysis of infections by bacteria such as Pseudomon...

ORGANISM(S): Caenorhabditis elegans

2011-01-01 | E-GEOD-21736 | biostudies-arrayexpress

Viruses

Detection of Human Viruses from wastewater sewage extracts

PRJNA106787 | ENA

DNA Microarray Platform for Detection and Surveillance of Viruses Transmitted by Small Mammals and Arthropods

Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. ...

ORGANISM(S): Aedes albopictus

2016-09-06 | E-GEOD-81392 | biostudies-arrayexpress

DNA Microarray Platform for Detection and Surveillance of Viruses Transmitted by Small Mammals and Arthropods

ORGANISM(S): Flavivirus

2016-09-05 | E-GEOD-81391 | biostudies-arrayexpress

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