Ubiquitin-like modifier

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Unknown (822)
Transcriptomics (721)
Proteomics (143)
Genomics (128)
Other (15)
Metabolomics (8)
Multiomics (2)

Organisms

Homo sapiens (320)
Mus musculus (210)
Arabidopsis thaliana (65)
Saccharomyces cerevisiae (55)
Drosophila melanogaster (23)
Rattus norvegicus (20)
Caenorhabditis elegans (13)
Danio rerio (11)
Oryza sativa (10)
Oncorhynchus mykiss (8)
Zea mays (6)
Bos taurus (6)
Canis lupus familiaris (6)
Sus scrofa (6)
Entamoeba histolytica (5)
Schizosaccharomyces pombe (5)
Saccharomyces cerevisiae SK1 (4)
Solea senegalensis (3)
Populus trichocarpa (3)
Cryptococcus neoformans (3)
Escherichia coli (3)
Oryza sativa Indica Group (2)
Lepidium sativum (2)
Medicago truncatula (2)
Salmo salar (2)
Oryza sativa Japonica Group (2)
Triticum aestivum (2)
Gallus gallus (2)
Corynebacterium glutamicum ATCC 13032 (2)
Triticum timopheevii (1)

Organisms

Homo sapiens (19)
Mus musculus (12)
Arabidopsis thaliana (3)
Drosophila melanogaster (1)
Rattus norvegicus (1)
Saccharomyces cerevisiae (1)

Repository

biostudies-arrayexpress (761)
MassIVE (61)
pride (51)
ENA (40)
geo (37)
EGA (18)
jPOST (16)
GPMDB (12)
iProX (9)
MetaboLights (8)
PanoramaPublic (3)

Tissue

Cell culture (12)
Epithelial cell (5)
Brain (2)
Cell suspension culture (2)
Stem cell (2)
Permanent cell line cell (2)
Kidney (2)
Liver (2)
Skeletal muscle tissue (1)
Diaphragm (1)
Pancreas (1)
Embryonic stem cell (1)
Ovary (1)
Plant cell (1)
Fibroblast (1)
Lung (1)
Monocyte (1)

Disease

Not Available (12)
Normal (3)
Melanoma (2)
Parkinson's disease (2)
Breast cancer (2)
Mock infection (1)
Psoriasis vulgaris (1)
B-cell chronic lymphocytic leukemia (1)
Chronic granulomatous disease (1)
IRAK-4 Q293X mutation (1)
ARR1-SRDX (1)
Spinocerebellar ataxia type 1 (1)
Temporal lobe epilepsy (1)
Exposed_Seronegative (1)
S enteritidis (1)
Osteosarcoma (1)
Ewing's sarcoma (1)
Neurodevelopmental delay (1)
Fetal akinesia deformation sequence syndrome (1)
Hematopoietic system disease (1)
Arthrogryposis multiplex congenita-1 (1)
Respiratory failure (1)
Diaphragm disease (1)
Severe congenital neutropenia (1)
Coronavirus infectious disease (1)
Cervix carcinoma (1)
Pancreatic cancer (1)
Acute leukemia (1)

Technology Type

Mass Spectrometry (51)
Shotgun proteomics (27)
Affinity purification coupled with mass spectrometry proteomics (16)
Bottom-up proteomics (10)
Data-dependent acquisition (8)
Gel-based experiment (6)
Chemical cross-linking coupled with mass spectrometry proteomics (6)
Mass spectrometry (5)
Mass spectrometry assay (3)
Illumina HumanCNV370, Illumina HumanHap 300 v2 Duo, Taqman and sequencing, Illumina Human660W-Quad (1)
Illumina HiSeq 2500 (1)
Illumina HiSeq 2000 (1)
Affinity proteomics (1)
SWATH MS (1)
Data-independent acquisition (1)

Instrument Platform

Illumina NovaSeq 6000 (29)
NextSeq 500 (16)
Illumina HiSeq 2500 (14)
Illumina HiSeq 4000 (12)
NextSeq 2000 (8)
NextSeq 550 (7)
Illumina HiSeq 2000 (7)
Illumina NovaSeq X (6)
Scanning hardware (5)
Element AVITI (3)
Ribo-Zero Gold (Illumina) (2)
Agilent 2100 Bioanalyzer (2)
Axon- GenePix4000B (2)
N/A (2)
Illumina MiSeq (2)
Chromium X instrument (10x Genomics); GEM-X FX Chips (10x Genomics); Agilent TapeStation D1000; qPCR (library quantification kit for Illumina platforms) (1)
Chromium X instrument (10x Genomics); GEM-X Flex Sample Preparation v2 Kit (10x Genomics; 1000781); Human Gene Expression Probe Set v1.0.1 (10x Genomics) (1)
Countess 3 FL Automated Cell Counter (Thermo Fisher Scientific; AMQAF2000); GEM-X Flex Sample Preparation v2 Kit (10x Genomics; 1000781) (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)
BD FACS ARIA III analyser (1)
CytoFLEX SRT Benchtop Cell Sorter (1)
Sony SH800S Cell Sorter (1)
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, (1)
10X Chromium On-Chip Multiplex (1)
10X Chromium Nuclei Isolation Kit (1)
Local workstation (1)
Chromium Single Cell 5' Library & Gel Bead Kit v2 (1)
FLOQSwab (Copan) (1)

Publication Date

2010 (99)
2013 (92)
2012 (71)
2015 (68)
2014 (67)
2011 (62)
2008 (58)
2016 (57)
2025 (54)
2009 (37)
2026 (34)
2024 (31)
2023 (31)
2007 (31)
2021 (28)
2017 (23)
2022 (21)
2018 (19)
2020 (18)
2019 (14)
2005 (11)
2006 (10)
2004 (2)

CHEBI ID

CHEBI:76078 (2)
CHEBI:136242 (1)
CHEBI:73223 (1)
CHEBI:136221 (1)
CHEBI:73208 (1)
CHEBI:136217 (1)
CHEBI:136174 (1)
CHEBI:136172 (1)
CHEBI:136165 (1)
CHEBI:136155 (1)
CHEBI:136159 (1)
CHEBI:134573 (1)
CHEBI:134555 (1)
CHEBI:134554 (1)
CHEBI:134553 (1)
CHEBI:136350 (1)
CHEBI:136349 (1)
CHEBI:136346 (1)
CHEBI:136344 (1)
CHEBI:136342 (1)
CHEBI:136341 (1)
CHEBI:136339 (1)
CHEBI:136338 (1)
CHEBI:136336 (1)
CHEBI:136334 (1)
CHEBI:136332 (1)
CHEBI:136331 (1)
CHEBI:136328 (1)
CHEBI:136326 (1)
CHEBI:136324 (1)

Metabolite Name

Acetylcarnitine (2)
PG(18:1/0:0) (1)
PE(P-16:0/22:1) (1)
PE(O-18:1/0:0) (1)
PE(18:1/22:0) (1)
PE(18:0/19:1) (1)
PE(16:1/18:0) (1)
PE(17:1/18:0) (1)
GM3(38:2) (1)
GM3(36:1) (1)
GM3(34:1) (1)
CL(20:2/16:1/18:1/18:3) (1)
CL(18:3/18:1/18:3/20:3) (1)
CL(18:2/18:2/18:2/18:3) (1)
PE(24:0/18:1) (1)
Arisugacin F (1)
Nanaomycin C (1)
Spicatolide E (1)
Gomisin L1 methyl ether (1)
5,7,4'-Trihydroxy-3'-methoxy-6,8-di-C-methylflavanone (1)
Gymnastatin E (1)
Confusarin (1)
3,4-Didehydroglabridin (1)
Leiocarpaquinone (1)
Sinensol E (1)
19-Hydroxysecochiliolide acid methyl ester (1)
Volkensine (1)
PHENPROCOUMON (1)
Gnetupendin A (1)
Nigrolineaxanthone H (1)

First Public Date

2023 (8)
2024 (6)
2021 (5)
2025 (4)
2022 (3)
2020 (3)
2014 (3)
2026 (2)
2017 (2)
2019 (1)
2018 (1)
2015 (1)
2013 (1)

Study type

Transcription profiling by array (475)
RNA-seq of coding RNA (94)
ChIP-seq (61)
RNA-seq of coding RNA from single cells (24)
Unknown experiment type (17)
ChIP-chip by array (13)
Comparative genomic hybridization by array (10)
Transcription profiling by SAGE (7)
Other (7)
ChIP-chip by tiling array (6)
High-throughput sequencing (4)
RNAi profiling by array (4)
RNA-seq of total RNA (4)
Transcription profiling by RT-PCR (3)
Proteomic profiling by array (3)
Genotyping by high throughput sequencing (3)
RNA-seq of non coding RNA (3)
CLIP-Seq (2)
Genotyping by array (2)
Single nucleus RNA sequencing (2)
MicroRNA profiling by array (2)
DNA-seq (2)
CUT&RUN (2)
Methylation profiling by high throughput sequencing (2)
Cell line - One-color microarray (1)
Animal - High-throughput sequencing (1)
Cell line - High-throughput sequencing (1)
Transcription profiling by tiling array (1)
Bisulfite-seq (1)
Hi-C (1)

Release Date

2013 (124)
2010 (121)
2016 (108)
2015 (104)
2014 (99)
2012 (98)
2011 (91)
2025 (87)
2021 (83)
2008 (79)
2022 (72)
2024 (67)
2020 (63)
2023 (60)
2017 (55)
2009 (53)
2019 (51)
2018 (49)
2007 (43)
2026 (27)
2006 (19)
2005 (19)
2004 (4)
2001 (2)
2000 (2)
2003 (1)
2002 (1)
1999 (1)

Lab affiliation

Institute for Research in Immunology and Cancer (IRIC) Université de Montréal, Department of Chemistry, Université de Montréal, MIL campus, Montréal, H2V 0B3, Canada (3)
Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas (FORTH), 100, Plastira Str., 70013 Heraklion, Crete, Greece. (2)
COI-NDM (University of Oxford) (2)
Instiute for Microbiology (1)
Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden (1)
1 Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada 2 Department of Chemistry, Université de Montréal, Montréal, Canada (1)
Department of Biology, University of Konstanz, 78457 Konstanz, Germany (1)
Department of Chemistry,University of Virginia,Charlottesville, VA 22903 USA (1)
College of Pharmaceutical Sciences Soochow University Yunxuan Building 1328 199 Ren'ai Road, Suzhou, Jiangsu 215123, China (1)
Chemical Cell Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands (1)
MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, Guangdong, China. (1)
CSIR—Centre for Cellular and Molecular Biology, Hyderabad-500007, TS, India (1)
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712 (1)
MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK (1)
Max-Planck-Insitute for Biochemistry, Department of cellular biochemistry (1)
Novartis Institutes for BioMedical Research, Basel, Switzerland (1)
CCB, LUMC, Netherlands (1)
Leiden University Medical Center (1)
University Magdeburg Institute of Exptl. Internal Medicine Leipziger STr. 44 39120 Magdeburg Germany (1)
Institute of Cancer Research, London & Wellcome Trust Sanger Institute (1)
Department of Biochemistry, UC Riverside (1)
Department of Cell & Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands (1)
Core Unit Proteomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany. (1)
Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine (1)
Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland (1)
Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium. Department for Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium. VIB Proteomics Core, VIB, 9000 Ghent, Belgium. (1)
Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149 Muenster (1)
Guangxi University (1)
Medical Research Council Protein Phosphorylation and Ubiquitylation Unit School of Life Sciences, University of Dundee, Dundee, Scotland (1)
Max-Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany University Clinical Center Goettingen, 37075 Goettingen, Germany (1)

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The conserved ubiquitin-like protein Hub1 plays a critical role in splicing in human cells

Different from canonical ubiquitin-like proteins, Hub1 does not form covalent conjugates with substrates but binds proteins non-covalently. In Saccharomyces cerevisiae, Hub1 associates with spliceosomes and mediates alternative splicing of SRC1, without affecting pre-mRNA splicing generally. Human H...

ORGANISM(S): Homo sapiens

2014-05-30 | E-GEOD-56878 | biostudies-arrayexpress

E2/E3-independent ubiquitin-like protein conjugation by Urm1 is directly coupled to cysteine persulfidation

Posttranslational modifications by ubiquitin-like proteins (UBL) are essential for nearly all cellular processes. Ubiquitin related modifier 1 (Urm1) is a non-canonical UBL which plays a key role in tRNA anticodon thiolation as a sulfur carrier protein (SCP). While Urm1 has also been observed to con...

ORGANISM(S): Chaetomium Thermophilum (ncbitaxon:209285) Saccharomyces Cerevisiae (ncbitaxon:4932) Homo Sapiens (ncbitaxon:9606)

2021-11-16 | MSV000088390 | MassIVE

Proteome-wide analysis of SUMO2 targets in response to pathological DNA replication stress in human cells

SUMOylation is a form of post-translational modification involving covalent attachment of SUMO (Small Ubiquitin-like Modifier) polypeptides to specific lysine residues in the target protein. In human cells, there are four SUMO proteins, SUMO1–4, with SUMO2 and SUMO3 forming a closely related subfami...

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

2017-03-28 | MSV000080699 | MassIVE

Proteome-wide identification of SUMO2 modification sites

Posttranslational modification with small ubiquitin-like modifiers (SUMOs) alters the function of proteins involved in diverse cellular processes. SUMOs are conjugated to lysine residues in target proteins by SUMO-specific enzymes. Although proteomic studies have identified hundreds of sumoylated su...

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

2017-03-29 | MSV000080741 | MassIVE

Urm1, not quite a ubiquitin-like modifier?

Not available

S-EPMC8561144 | biostudies-literature

Structural analysis of UBL5, a novel ubiquitin-like modifier.

Not available

S-EPMC2323916 | biostudies-literature

Genome-wide analysis of insulin-like growth factor 1 receptor (IGF1R) binding sites in DFB cells

The insulin-like growth factor 1 receptor (IGF-1R) plays crucial roles in developmental and cancer biology. Most of its biological effects have been ascribed to its tyrosine kinase activity. We report that IGF-1 promotes the modification of IGF-1R by small ubiquitin-like modifier protein-1 (SUMO-1) ...

ORGANISM(S): Homo sapiens

2010-08-25 | E-GEOD-23792 | biostudies-arrayexpress

Multiple Arkadia/RNF111 structures coordinate its Polycomb body association and transcriptional control

The RING domain protein Arkadia/RNF111 is a ubiquitin ligase in the transforming growth factor beta (TGFβ) pathway. We previously identified Arkadia as a small ubiquitin-like modifier (SUMO)-binding protein with clustered SUMO-interacting motifs (SIMs) that together form a SUMO-binding domain (SBD)....

ORGANISM(S): Mus musculus

2015-02-11 | E-GEOD-65796 | biostudies-arrayexpress

Involvement of a eukaryotic-like ubiquitin-related modifier in the proteasome pathway of the archaeon Sulfolobus acidocaldarius.

Not available

S-EPMC4569737 | biostudies-literature

Conjugation of the ubiquitin activating enzyme UBE1 with the ubiquitin-like modifier FAT10 targets it for proteasomal degradation.

Not available

S-EPMC4359146 | biostudies-literature