E3 - OmicsDI

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Transcriptomics (2960)
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Organisms

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Mus musculus (724)
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synthetic construct (8)
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Lodderomyces elongisporus NRRL YB-4239 (5)
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Organisms

Homo sapiens (511)
Mus musculus (365)
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Gymnomyces sp. KIS8 (3)
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Mus (2)
plant metagenome (2)

Repository

biostudies-arrayexpress (2385)
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geo (1026)
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pride (938)
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Instrument Platform

Illumina NovaSeq 6000 (142)
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NA (5)
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Illumina HiSeq 3000 (4)
Axon- GenePix4000B (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)
Sequel IIe (2)
Single cells were captured using the 10x Genomics Chromium Controller. (2)
Chromium Controller (2)
PromethION (2)
10x Genomics Chromium (2)
Ribo-Zero Gold (Illumina) (2)

Publication Date

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2010 (413)
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2007 (101)
2017 (90)
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UNIPROT ID/AC

G3P1_ECOLI (7)
DAPA_ECOLI (7)
RHLB_ECOLI (7)
KDPD_ECOLI (7)
CYDA_ECOLI (7)
DCRB_ECOLI (7)
PPSA_ECOLI (7)
SECA_ECOLI (7)
BIPA_ECOLI (7)
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METB_ECOLI (7)
GLYA_ECOLI (7)
GHRB_ECOLI (7)
HLDD_ECOLI (7)
SECB_ECOLI (7)
DPPA_ECOLI (7)
ACKA_ECOLI (7)
YQAB_ECOLI (7)
PSTS_ECOLI (7)
HSLO_ECOLI (7)
EX3_ECOLI (7)
CLPA_ECOLI (7)
DCYD_ECOLI (7)

CHEBI ID

CHEBI:15428 (23)
CHEBI:17191 (22)
CHEBI:16977 (21)
CHEBI:17203 (21)
CHEBI:17895 (20)
CHEBI:17295 (20)
CHEBI:32816 (20)
CHEBI:16828 (19)
CHEBI:17196 (19)
CHEBI:16414 (19)
CHEBI:16015 (19)
CHEBI:17596 (19)
CHEBI:16335 (19)
CHEBI:17368 (19)
CHEBI:16857 (18)
CHEBI:16467 (18)
CHEBI:17053 (18)
CHEBI:30769 (18)
CHEBI:17568 (18)
CHEBI:15741 (18)
CHEBI:16027 (17)
CHEBI:17115 (17)
CHEBI:18050 (17)
CHEBI:15603 (17)
CHEBI:15756 (17)
CHEBI:30915 (17)
CHEBI:16643 (16)
CHEBI:16761 (12)
CHEBI:15422 (10)
CHEBI:26523 (1)

Metabolite Name

L-Phenylalanine (22)
Adenosine (21)
L-Histidine (20)
L-Proline (20)
Inosine (20)
Betaine (19)
Uracil (18)
Hypoxanthine (18)
L-Asparagine (18)
L-Leucine (18)
Xanthine (18)
Thymine (17)
L-Tyrosine (17)
L-Glutamine (17)
Ornithine (16)
Guanine (16)
L-Lysine (16)
L-Alanine (16)
L-Threonine (16)
L-Isoleucine (16)
Cytidine (16)
D-Glucose (15)
Taurine (15)
L-Arginine (15)
Palmitic acid (14)
Cytosine (14)
Adenine (14)
Creatine (14)
L-Methionine (14)
L-Valine (14)

First Public Date

2025 (228)
2026 (224)
2024 (223)
2020 (133)
2023 (115)
2022 (106)
2021 (103)
2014 (100)
2019 (62)
2018 (54)
2017 (49)
2016 (28)
2015 (23)
2013 (17)

Modelling Approach

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

Study status

Completed (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 (82)
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)
Institute of Molecular Biology (IMB), Mainz, Germany (5)
Northwestern University, Department of Chemistry (5)
Department of Cell & Developmental Biology, University of California, San Diego, La Jolla, CA (4)
Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas (4)
Director, Institute of Biochemistry II Goethe University Medical Faculty University Hospital Building 75 Theodor-Stern-Kai 7 60590 Frankfurt am Main Germany (4)
Principal Investigator Centre for Targeted Protein Degradation, School of Life Sciences (4)
ETHZ IMSB (4)
Harvard Medical School (4)
The University of Melbourne (4)
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)
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)
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)
Department of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA (3)
Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland (3)
IBC R602,128, Academia Road Sec. 2, Nankang, Taipei 115, Taiwan (3)
Professor Institute of Biochemistry II Goethe University Medical Faculty University Hospital Building 75 Theodor-Stern-Kai 7 60590 Frankfurt am Main Germany (3)
Edinburgh Cancer Research, CRUK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK (3)
Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany (3)
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, United States (3)
Cambridge Institute for Medical Research, University of Cambridge (3)
University of Edinburgh (3)
Head of the Curie Institute Mass Spectrometry Platform (3)
Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany (2)

Keyword

Colorectal Neoplasm (1)

IsPrivate

False (2)

Classification

bacteria (12)
fungi (3)
viruses (3)
protozoa (1)

Modification

2x(15)N labeled L-lysine (3)
4x(15)N labeled L-arginine (2)
Light form - site K (1)
Heavy form - site K (1)
79.966331 (1)
42.010565 (1)
15.994915 (1)
N6-dimethyl-L-lysine (1)
57.021464 (1)
4-tetrahydrothiazine-3-carboxylic acid (1)

Study type

Transcription profiling by array (1239)
Unknown experiment type (354)
RNA-seq of coding RNA (211)
RNA-seq of coding RNA from single cells (125)
ChIP-seq (111)
Comparative genomic hybridization by array (66)
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Methylation profiling by array (14)
High-throughput sequencing (10)
Single nucleus RNA sequencing (9)
RNA-seq of non coding RNA (9)
Animal - High-throughput sequencing (8)
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Exome sequencing (3)
CUT&RUN (3)
Methylation profiling by high throughput sequencing (3)
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Spatial transcriptomics by high-throughput sequencing (2)

Release Date

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2006 (180)
2004 (29)
2002 (28)
2003 (26)
1999 (11)
2001 (8)
2000 (8)
1998 (6)
1997 (1)

Location

United States (1)

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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

Calenduloside E produced by Bifidobacterium animalis B960 increases glibenclamide efficacy and alleviates drug-induced adverse effects via the IRS1/PI3K/AKT signaling pathway in a type 2 diabetes model Calenduloside E produced by Bifidobacterium animalis B960 increases glibenclamide efficacy and alleviates drug-induced adverse effects via the IRS1/PI3K/AKT signaling pathway in cell, organ-on-a-chip, and mouse models of type 2 diabetes.

Glibenclamide (GLIB), a type 2 diabetes therapy, has long-term safety concerns. Probiotic–drug coadministration, an emerging adjunctive approach for metabolic diseases, improves therapeutic outcomes and side effects. Here, Bifidobacterium animalis B960 was selected from 71 probiotic strains by HP...

2025-07-08 | MTBLS12697 | MetaboLights

Variovorax sp. E3 strain:E3

Variovorax sp. E3 strain:E3 Genome sequencing and assembly

PRJNA352329 | ENA

Arthrobacter sp. E3 strain:E3

Arthrobacter sp. E3 strain:E3 Genome sequencing and assembly

PRJNA693417 | ENA

Aliiglaciecola lipolytica E3 strain:E3

draft genome of Glaciecola lipolytica E3

PRJDB25 | ENA

Escherichia coli strain:E3

Escherichia coli strain:E3 Genome sequencing

PRJNA1422671 | ENA

Halogeometricum borinquense strain:E3

Halogeometricum borinquense strain:E3 Genome sequencing

PRJNA1029887 | ENA

Saccharopolyspora erythraea strain:E3

Saccharopolyspora erythraea strain:E3 Genome sequencing and assembly

PRJNA634475 | ENA

Pediococcus pentosaceus strain:E3

Pediococcus pentosaceus strain:E3 Genome sequencing and assembly

PRJNA1010379 | ENA

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

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