E3-ligase - OmicsDI

Show results for

Unknown (8720)
Genomics (2276)
Transcriptomics (1096)
Proteomics (1060)
Other (73)
Metabolomics (22)
Methylation profiling (17)
Models (3)
Multiomics (1)

Organisms

Homo sapiens (1753)
Mus musculus (468)
Arabidopsis thaliana (83)
Drosophila melanogaster (47)
Saccharomyces cerevisiae (46)
Escherichia coli (22)
Rattus norvegicus (22)
Caenorhabditis elegans (18)
Oryza sativa (17)
Danio rerio (9)
Escherichia coli str. K-12 substr. MG1655 (7)
Escherichia coli K-12 (6)
Lodderomyces elongisporus NRRL YB-4239 (5)
Ovis aries (5)
Cryptococcus gattii (4)
Candida albicans (4)
Sus scrofa (4)
Mycolicibacterium smegmatis MC2 155 (3)
Heterocephalus glaber (3)
Gallus gallus (3)
Lodderomyces elongisporus (2)
Pan troglodytes (2)
Eukaryota (1)
Candidozyma auris (1)
Chamaelirium luteum (1)
Kluyveromyces marxianus (1)
Pseudomonas protegens (1)
Equus asinus (1)
Mus musculus castaneus (1)
Rhodopseudomonas palustris (1)

Organisms

Homo sapiens (447)
Mus musculus (278)
Arabidopsis thaliana (43)
Saccharomyces cerevisiae (32)
Drosophila melanogaster (16)
Caenorhabditis elegans (11)
Rattus norvegicus (11)
Oryza sativa (9)
Schizosaccharomyces pombe (6)
Danio rerio (5)
Marchantia polymorpha (3)
Mus (2)
Triticum aestivum (2)
Helicoverpa zea (1)
Saccharomyces cerevisiae W303 (1)
Loxodonta africana (1)
Cryptococcus neoformans H99 (1)
Mesocricetus auratus (1)
Cryptococcus neoformans (1)
Megalobrama amblycephala (1)
Tetrahymena thermophila (1)
Macaca fascicularis (1)
Verticillium dahliae (1)
Rosa hybrid cultivar (1)
Setaria italica (1)
Saccharomyces cerevisiae BY4741 (1)
Solanum lycopersicum (1)
Bombyx mori (1)
Ciona intestinalis (1)
Ipomoea batatas (1)

Repository

ENA (1064)
EGA (956)
geo (867)
pride (739)
biostudies-arrayexpress (573)
iProX (142)
MassIVE (119)
jPOST (49)
MetaboLights (21)
PanoramaPublic (7)
GPMDB (4)
ExpressionAtlas (2)
BioModels (2)
Cell Collective (1)
MetabolomicsWorkbench (1)

Tissue

Cell culture (270)
Epithelial cell (48)
Permanent cell line cell (41)
Kidney (21)
Brain (17)
T cell (17)
Blood (16)
Embryonic stem cell (14)
Fibroblast (14)
Plant cell (14)
Leaf (12)
Blood cell (11)
HeLa cell (11)
Cell suspension culture (10)
Kidney cell (9)
Liver (9)
B cell (8)
Early embryonic cell (8)
Hepatocyte (7)
Macrophage (7)
Bone marrow (6)
Spleen (6)
Embryo (5)
Leukocyte (5)
Stem cell (5)
Egg (4)
Erythrocyte (4)
HEK-293T cell (4)
Lung (4)
Tumor cells (1)

Disease

Disease free (23)
Acute leukemia (20)
Breast cancer (11)
Colon cancer (8)
Multiple myeloma (6)
Neuroblastoma (5)
Lymphoma (5)
Not Available (4)
Amyotrophic lateral sclerosis (4)
Cervix carcinoma (4)
Human immunodeficiency virus infectious disease (4)
Brain cancer (3)
Cervical adenocarcinoma (3)
Chronic myeloid leukemia (3)
Human cytomegalovirus infection (3)
Pancreatic cancer (3)
Angelman syndrome (2)
Autism spectrum disorder (2)
Glioblastoma (2)
Kidney cancer (2)
Parkinson's disease (2)
Prostate adenocarcinoma (2)
Skin melanoma (2)
Trypanosomiasis (2)
Neurodegenerative disease (1)
Non-infected (1)
Psoroptes ovis infestation (1)
Osteosarcoma (1)
Cancer (1)
COVID-19 (1)

Technology Type

Mass Spectrometry (740)
Shotgun proteomics (286)
Affinity purification coupled with mass spectrometry proteomics (166)
Bottom-up proteomics (163)
Data-dependent acquisition (87)
Data-independent acquisition (70)
Gel-based experiment (60)
Chemical cross-linking coupled with mass spectrometry proteomics (37)
SWATH MS (20)
Top-down proteomics (10)
Illumina HiSeq 2000 (9)
Mass spectrometry assay (9)
Mass spectrometry (8)
Illumina HiSeq 2000, ILLUMINA (3)
NMR spectroscopy assay (2)
NMR spectroscopy (2)
Illumina MiSeq, Illumina HiSeq 2500, ILLUMINA (1)
Infinium Omni2.5M (1)
Agilent 8x60K (1)
Illumina HumanCoreExome-12v1-0_A and HumanCoreExome-24v1-0_A, Illumina Human670-QuadCustom_v1_A (1)
Illumina_450K, Illumina_HumanHT-12_V4, ILLUMINA, Illumina HiSeq 2000 (1)
CAPILLARY, AB 3730xL Genetic Analyzer (1)
454 GS FLX Titanium, Illumina HiSeq 2000 (1)
ZCall, Illumina HumanExome-12v1_A-GenCall (1)
Illumina HiSeq 2500 (1)
Illumina 1.2M, Affymetrix 6.0, Human670-QuadCustom v1 (1)
Illumina HumanExome-12v1_A-GenCall, zCall, GenoSNP, - Illuminus (1)
Illumina MiSeq (1)
Illumina Genome Analyzer II (1)
ESI (1)

Instrument Platform

Illumina NovaSeq 6000 (114)
NextSeq 500 (27)
NextSeq 2000 (22)
Illumina NovaSeq X (20)
NextSeq 550 (15)
BGISEQ-500 (14)
Illumina HiSeq 4000 (13)
Illumina HiSeq 2000 (11)
Illumina HiSeq 2500 (8)
NextSeq 1000 (7)
NA (5)
N/A (5)
DNBSEQ-T7 (5)
Element AVITI (4)
10x Genomics Chromium Controller (4)
DNBSEQ-G400 (4)
Axon- GenePix4000B (3)
GenePix 4000B [Axon Instruments] (3)
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. (2)
Single cells were captured using the 10x Genomics Chromium Controller. (2)
Chromium Controller (2)
10x Genomics Chromium (2)
Ribo-Zero Gold (Illumina) (2)
None (2)
Agilent 2100 Bioanalyzer (2)
BAS-5000 [FUJIFILM] (2)
Illumina HiSeq X (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)

Publication Date

2025 (477)
2026 (432)
2024 (295)
2021 (187)
2023 (185)
2022 (177)
2020 (143)
2019 (80)
2010 (75)
2015 (67)
2018 (65)
2017 (50)
2013 (46)
2014 (43)
2016 (42)
2012 (35)
2011 (31)
2008 (29)
2007 (18)
2009 (17)
2006 (10)
2005 (8)

CHEBI ID

CHEBI:17750 (5)
CHEBI:15891 (5)
CHEBI:18050 (5)
CHEBI:17203 (5)
CHEBI:16015 (5)
CHEBI:17196 (5)
CHEBI:16977 (5)
CHEBI:17191 (5)
CHEBI:16857 (4)
CHEBI:18183 (4)
CHEBI:17115 (4)
CHEBI:16283 (4)
CHEBI:15729 (4)
CHEBI:16467 (4)
CHEBI:15428 (4)
CHEBI:17053 (4)
CHEBI:30915 (4)
CHEBI:16737 (4)
CHEBI:16919 (4)
CHEBI:16347 (4)
CHEBI:16414 (4)
CHEBI:15603 (4)
CHEBI:17895 (4)
CHEBI:17295 (4)
CHEBI:37054 (3)
CHEBI:64552 (3)
CHEBI:15422 (1)
CHEBI:16761 (1)
CHEBI:16027 (1)
CHEBI:26523 (1)

Metabolite Name

Betaine (10)
Creatine (9)
Choline (8)
Glycerophosphocholine (8)
Uracil (7)
Pyridoxine (7)
L-Histidine (7)
Guanine (7)
L-Glutamine (7)
Cytidine (7)
Xanthine (7)
Creatinine (7)
L-Phenylalanine (7)
Thiamine (6)
L-Asparagine (6)
L-Ornithine (6)
Acetylcholine (6)
Taurine (6)
Pantothenic acid (6)
L-Proline (6)
Tyramine (6)
Riboflavin (6)
L-Carnitine (6)
L-Isoleucine (6)
L-Leucine (6)
Hypoxanthine (6)
D-Fructose (5)
L-Aspartate (5)
D-Galactose (5)
L-Cystine (5)

First Public Date

2026 (187)
2024 (175)
2025 (172)
2023 (82)
2022 (79)
2021 (79)
2020 (79)
2014 (61)
2019 (40)
2017 (35)
2018 (27)
2016 (22)
2015 (16)
2013 (10)

Modelling Approach

Differential equation model (1)
Ordinary differential equation model (1)

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 (73)
Department of Chemistry and Chemical Biology, Harvard University (9)
Dr. Matthias Gstaiger ETH Zürich Institute of Molecular Systems Biology Otto-Stern-Weg 3 8093 Zürich Switzerland (5)
ETH Zürich Institute of Molecular Systems Biology HPM F43 Otto-Stern-Weg 3 8093 Zürich Switzerland (5)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (5)
Department of Cell & Developmental Biology, University of California, San Diego, La Jolla, CA (4)
ETHZ IMSB (4)
Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas (4)
Institute of Molecular Biology (IMB), Mainz, Germany (4)
Principal Investigator Centre for Targeted Protein Degradation, School of Life Sciences (4)
The University of Melbourne (4)
Cambridge Institute for Medical Research, University of Cambridge (3)
Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany (3)
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA (3)
Department of Orthopedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Hangzhou City, China. (3)
Department of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA (3)
Edinburgh Cancer Research, CRUK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK (3)
Head of the Curie Institute Mass Spectrometry Platform (3)
IBC R602,128, Academia Road Sec. 2, Nankang, Taipei 115, Taiwan (3)
Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany. (3)
Laboratoire Maladies Rares: Génétique et Métabolisme- INSERM U1211, 33000 Bordeaux, France (3)
Northwestern University, Department of Chemistry (3)
Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, Collaborative Innovation Center of Hematology, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China (3)
1. Key Laboratory of Photoelectric Conversion and Utilization of Solar Energy, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China. 2. Shandong Energy Institute, Qingdao 266101, China. 3. Qingdao New Energy Shandong Laboratory, Qingdao 266101, China. (2)
1Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China (2)
Amphista Therapeutics Cambridge United Kingdom (2)
Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK (2)
Cancer Research UK Scotland Institute (Formerly the Cancer Research UK Beatson Institute) Garscube Estate Switchback Road Bearsden Glasgow, G61 1BD (2)
Center for Cell Signaling Department of Biochemistry & Molecular Genetics University of Virginia, Charlottesville, VA, USA (2)
Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany (2)

IsPrivate

False (2)

Classification

fungi (2)
protozoa (1)
bacteria (1)

Modification

2x(15)N labeled L-lysine (2)
4x(15)N labeled L-arginine (2)
Heavy form - site K (1)
Light form - site K (1)

Study type

Transcription profiling by array (220)
RNA-seq of coding RNA from single cells (110)
RNA-seq of coding RNA (79)
ChIP-seq (66)
Transcription profiling by tiling array (14)
DNA-seq (13)
Comparative genomic hybridization by array (11)
Unknown experiment type (9)
RNA-seq of total RNA (9)
Single nucleus RNA sequencing (8)
ATAC-seq (5)
ChIP-chip by tiling array (4)
Hi-C (4)
Exome sequencing (3)
Transcription profiling by RT-PCR (2)
Spatial transcriptomics by high-throughput sequencing (2)
Other (2)
Proteomic profiling by array (2)
CUT&RUN (2)
Transcription profiling by SAGE (1)
Animal - High-throughput sequencing (1)
RNAi profiling by array (1)
ChIP-chip by array (1)
Bisulfite-seq (1)
RIP-seq (1)
Methylation profiling by array (1)
RNA-seq of non coding RNA (1)

Release Date

2025 (1025)
2022 (835)
2023 (816)
2024 (814)
2021 (767)
2020 (671)
2019 (516)
2017 (475)
2018 (469)
2015 (399)
2016 (387)
2014 (359)
2013 (301)
2026 (268)
2010 (243)
2012 (234)
2011 (215)
2009 (145)
2008 (118)
2007 (89)
2006 (41)
2005 (36)
2004 (19)
2003 (18)
2002 (10)
2001 (4)
1999 (4)
2000 (3)
1998 (1)

Previous page
1 / 1327
You're on page 1
page 2
page 3
page 4
page 5
page ...
page 1327
Next page

Sort by:

Relevance

Page size

ACSS2 Regulates HIF-2α Degradation through the E3-Ubiquitin Ligase MUL1 in Clear Cell Renal Cell Carcinoma

Not available

ORGANISM(S): Mus musculus

ST002241 | MetabolomicsWorkbench

Merlin/NF2 Suppresses Tumorigenesis by Inhibiting the E3 Ubiquitin Ligase CRL4DCAF1 in the Nucleus

Current models imply that the FERM domain protein Merlin, encoded by the tumor suppressor NF2, inhibits mitogenic signaling at or near the plasma membrane. Here, we show that the closed, growth inhibitory form of Merlin accumulates in the nucleus, binds to the E3 ubiquitin ligase CRL4DCAF1, and supp...

ORGANISM(S): Mus musculus

2010-03-09 | E-GEOD-19305 | biostudies-arrayexpress

Supporting raw MS data for paper (doi:10.1038/s41589-025-01894-4) by Raiff A., Zhao Z. et al (2025), titled "TOM20-Driven E3 Ligase Recruitment Regulates Mitochondrial Dynamics Through PLD6"

Supporting raw MS data for paper (doi:10.1038/s41589-025-01894-4) by Raiff A., Zhao Z. et al (2025), titled "TOM20-Driven E3 Ligase Recruitment Regulates Mitochondrial Dynamics Through PLD6". Index of MS files and labels Supplementary Table 1 - HEK293T - Proteome (CZ-1-23 | Unimod:35; 737; 4 | 126 -...