Ubiquitin-binding domain

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Unknown (1965)
Transcriptomics (575)
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Metabolomics (4)
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Organisms

Homo sapiens (276)
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Saccharomyces cerevisiae (26)
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Organisms

Homo sapiens (39)
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Repository

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Disease

Breast cancer (3)
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S enteritidis (1)
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Technology Type

Mass Spectrometry (83)
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Affinity purification coupled with mass spectrometry proteomics (22)
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Chemical cross-linking coupled with mass spectrometry proteomics (6)
Gel-based experiment (4)
Data-independent acquisition (3)
SWATH MS (3)
Top-down proteomics (3)
Mass spectrometry assay (2)
Illumina HiSeq 2000 (1)
NMR spectroscopy assay (1)
Mass spectrometry (1)
HDMSE (1)

Instrument Platform

Illumina NovaSeq 6000 (37)
NextSeq 500 (18)
Illumina HiSeq 2500 (10)
NextSeq 550 (7)
Illumina HiSeq 4000 (7)
NextSeq 2000 (6)
Illumina HiSeq 2000 (6)
Scanning hardware (4)
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Axon- GenePix4000B (3)
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BGISEQ-500 (2)
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UC Irvine HPC (1)
Bioanalyzer, Nanodrop, (1)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Cell culture (1)
STAR v2.5.3a, rpkmforgenes, RSeQC 2.6.1 (1)
Illumina Nextera XT index kits (Set A–D) (1)
Oligo(dT) primer and SuperScript II reverse transcriptase (ThermoFisher Scientific), TapeStation 4200 or 2100 Bioanalyzer with a DNA High Sensitivity chip (Agilent Biotechnologies) (1)
Aria III (BD Biosciences) (1)
Chromium Next GEM Chip G (1)
Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis. (1)
Described in protocol (1)
IEO HPC (1)
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, (1)
Chromium Controller / Agilent Bioanalyzer (1)

Publication Date

2010 (87)
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2014 (59)
2013 (55)
2012 (52)
2011 (52)
2015 (49)
2008 (45)
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2026 (42)
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2023 (30)
2016 (26)
2018 (25)
2007 (24)
2021 (23)
2009 (19)
2020 (18)
2019 (15)
2017 (10)
2006 (8)
2005 (7)
2004 (3)

CHEBI ID

CHEBI:37054 (1)
CHEBI:64552 (1)
CHEBI:37714 (1)
CHEBI:13705 (1)
CHEBI:28847 (1)
CHEBI:15361 (1)
CHEBI:24996 (1)
CHEBI:31011 (1)
CHEBI:4153 (1)
CHEBI:40410 (1)
CHEBI:60645 (1)
CHEBI:16530 (1)
CHEBI:16283 (1)
CHEBI:15729 (1)
CHEBI:16870 (1)
CHEBI:16977 (1)
CHEBI:4139 (1)
CHEBI:4208 (1)
CHEBI:15428 (1)
CHEBI:17754 (1)
CHEBI:18147 (1)
CHEBI:4167 (1)
CHEBI:17268 (1)
CHEBI:17196 (1)
CHEBI:17115 (1)
CHEBI:17750 (1)
CHEBI:16467 (1)
CHEBI:17203 (1)
CHEBI:15891 (1)
CHEBI:18183 (1)

Metabolite Name

L-GlutamicAcid (1)
2-Hydroxyisovalerate (1)
3-Hydroxybutyrate (1)
2-Hydroxybutyrate (1)
2-Oxoisovalerate (1)
L-Glycine (1)
TMAO (1)
Valerate (1)
D-Fucose (1)
L-Aspartate (1)
Myo-Inositol (1)
D-Galactose (1)
D-Fructose (1)
L-Cystine (1)
D-Glucose (1)
2-Oxoglutarate (1)
Glycerol (1)
L-Alanine (1)
Acetoacetate (1)
Pyroglutamate (1)
Betaine (1)
D-Maltose (1)
L-Proline (1)
N-Acetylglycine (1)
L-Arginine (1)
L-Asparagine (1)
L-Ornithine (1)
L-Threonine (1)
Taurine (1)
Lactate (1)

First Public Date

2026 (12)
2024 (12)
2025 (10)
2022 (10)
2023 (7)
2020 (6)
2014 (6)
2021 (4)
2019 (4)
2018 (3)
2017 (3)
2015 (2)

Study type

Transcription profiling by array (331)
RNA-seq of coding RNA (82)
ChIP-seq (35)
RNA-seq of coding RNA from single cells (29)
Comparative genomic hybridization by array (9)
Methylation profiling by array (9)
RNA-seq of non coding RNA (9)
Unknown experiment type (8)
ChIP-chip by tiling array (8)
RNA-seq of total RNA (8)
Transcription profiling by SAGE (6)
Transcription profiling by RT-PCR (5)
Other (5)
Methylation profiling by high throughput sequencing (5)
ChIP-chip by array (4)
Genotyping by array (3)
Transcription profiling by tiling array (2)
RIP-seq (2)
RNA-seq of non coding RNA from single cells (1)
High-throughput sequencing (1)
Human - One-color microarray (1)
Animal - High-throughput sequencing (1)
Cell line - High-throughput sequencing (1)
RNAi profiling by array (1)
Hi-C (1)
Ribo-seq (1)
Single nucleus RNA sequencing (1)
MicroRNA profiling by array (1)
DNA-seq (1)
Proteomic profiling by array (1)

Release Date

2025 (183)
2010 (167)
2015 (157)
2014 (157)
2022 (152)
2021 (131)
2013 (131)
2012 (130)
2016 (128)
2024 (124)
2019 (124)
2011 (124)
2023 (122)
2020 (112)
2018 (109)
2017 (100)
2008 (91)
2009 (77)
2007 (61)
2026 (41)
2006 (36)
2005 (27)
2004 (19)
2003 (10)
2002 (8)
2001 (5)
1998 (4)
2000 (3)
1999 (2)

Lab affiliation

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA (4)
Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany (2)
ETH Zurich (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)
The University of Melbourne (2)
center for biochemistry, University of cologne (2)
1Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA 92093 (1)
Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany (1)
Biology department, Washington University in Saint Louis, Saint Louis, MO, USA (1)
Bowling Green State University (1)
CRUK Beatson Institute, Switchback Road, Glasgow G61 1BD, UK. (1)
CSO, Structural Genomics Consortium Professor, Medical Biophysics, University of Toronto Sr. Scientist, Princess Margaret Cancer Centre (1)
Chinese Academy of Medical Sciences Oxford Institute (CAMS) - Nuffield Department of Medicine. University of Oxford (1)
College of Pharmaceutical Sciences Soochow University Yunxuan Building 1328 199 Ren'ai Road, Suzhou, Jiangsu 215123, China (1)
Department of Biochemistry and Molecular Biology. University of the Basque Country (EHU) (1)
Department of Biochemistry, University of Washington, Seattle, WA, USA (1)
Department of Biological Sciences, Kent State University, USA (1)
Department of Cell & Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands (1)
Department of Cell Biology Harvard Medical School Boston, MA USA (1)
Department of Chemistry & Chemical biology, Northeastern University (1)
Department of Chemistry,University of Virginia,Charlottesville, VA 22903 USA (1)
Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA (1)
Department of Medicine, Department of Microbiology & Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. (1)
Department of Molecular Biology, Princeton University, USA (1)
Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland. (1)
Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Germany (1)
Department of Psychiatry and Human Behavior University of California Irvine 4056 Gross Hall/ Stem Cell Research Center 845 Health Sciences Road Irvine, CA 92697-1705 (1)
Department of Psychiatry and Human Behavior University of California, Irvine Irvine, CA 92697, USA (1)
Director of Proteomics Core Facility, Children's Hospital of Philadelphia, Philadelphia, PA USA (1)
Discovery Biology, AstraZeneca Pharmaceuticals (1)

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Mass spectrometry insights into a tandem ubiquitinâ??binding domain hybrid engineered for the selective recognition of unanchored polyubiquitin

Unanchored polyubiquitin chains are emerging as important regulators of cellular physiology with diverse roles paralleling those of substrate-conjugated polyubiquitin. However tools able to discriminate unanchored polyubiquitin chains of different isopeptide linkages have not been described. We desc...

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

2016-07-22 | MSV000079990 | MassIVE

Asparagine hydroxylation of the UBA domain in Cezanne (OTUD7B)

by DUBs need to be tightly controlled. Here, we identify asparagine hydroxylation as a novel posttranslational modification involved in the regulation of Cezanne (OTUD7B), a DUB that controls key cellular functions and signaling pathways. We demonstrate that Cezanne is a substrate for FIH1- and oxyg...

ORGANISM(S): Homo sapiens (Human)

2020-01-24 | PXD015216 | Pride

Mass spectrometry insights into a tandem ubiquitin‐binding domain hybrid engineered for the selective recognition of unanchored polyubiquitin

ORGANISM(S): Homo sapiens (Human)

2016-05-18 | PXD004059 | Pride

Ubiquitin Polyubiquitin

Quantitative XL-MS Analysis of HHARI in the presence or absence of 4EHP

RING-Between-RING (RBR) E3 ligases mediate ubiquitin transfer through an obligate E3- ubiquitin thioester intermediately prior to substrate ubiquitination. While RBRs share a conserved catalytic module, substrate recruitment mechanisms remain enigmatic and the relevant domains have yet to be identi...

ORGANISM(S): Homo Sapiens

PXD030871 | panorama

CoCUN, a Novel Ubiquitin Binding Domain Identified in N4BP1.

Not available

S-EPMC6681339 | biostudies-literature

An ankyrin-repeat ubiquitin-binding domain determines TRABID's specificity for atypical ubiquitin chains.

Not available

S-EPMC5260945 | biostudies-literature

The Ubiquitin Interacting Motif Like Domain of Met4 is a K48 Polyubiquitin Chain Selective Binding Domain

Publication upload for journal submission 'The Ubiquitin Interacting Motif Like Domain of Met4 is a K48 Polyubiquitin Chain Selective Binding Domain'

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

2021-02-02 | MSV000086795 | MassIVE