Ribosomal dna repair

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Transcriptomics (383)
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Disease

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Technology Type

Mass Spectrometry (19)
Affinity purification coupled with mass spectrometry proteomics (6)
Shotgun proteomics (6)
Bottom-up proteomics (4)
Mass spectrometry assay (3)
Gel-based experiment (2)
Data-dependent acquisition (2)
ILLUMINA, Illumina HiSeq 2500 (1)
Illumina HiSeq 2000 (1)
Illumina HiSeq 2000, ILLUMINA (1)
Affinity proteomics (1)
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Chemical cross-linking coupled with mass spectrometry proteomics (1)
Data-independent acquisition (1)

Instrument Platform

Illumina NovaSeq 6000 (26)
Illumina HiSeq 2500 (17)
NextSeq 500 (13)
Illumina HiSeq 2000 (12)
Illumina HiSeq 4000 (9)
Illumina NovaSeq X (8)
BGISEQ-500 (6)
Illumina MiSeq (6)
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)
10X Genomics Chromium (2)
NextSeq 2000 (2)
HiSeq X Ten (2)
Chromium Next GEM Chip G (1)
10X v3 (1)
STAR (1)
Single Cell/Low Input RNA Library Prep Kit for Illumina (#E6420S, New England Biolabs) (1)
RNA Micro Kit (Qiagen). (1)
Thermal cycler, Agilent BioAnalyzer 2100 (1)
Microcentrifuge, vortex spinner, pipettes, -80C freezer (1)
Zeiss Stereomicroscope, standard lab plasticware (1)
Thermal cycler; magnetic separation rack; Qubit Fluorometer; Agilent TapeStation 4200 (1)
Microcentrifuge; magnetic separation rack; Qubit Flu/spectrophotometer; Agilent TapeStation 4200 (1)
Incubator shaker; spectrophotometer; Cmag measurement system; flow cytometer (1)
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Publication Date

2015 (56)
2013 (49)
2014 (48)
2026 (37)
2012 (35)
2016 (29)
2025 (28)
2010 (28)
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2011 (18)
2022 (15)
2017 (13)
2020 (12)
2018 (11)
2008 (9)
2019 (6)
2009 (6)
2007 (6)
2006 (4)
2005 (2)

UNIPROT ID/AC

ARI1_YEAST (1)
H3_YEAST (1)
OYE2_YEAST (1)
ACON_YEAST (1)
TPS2_YEAST (1)
REB1_YEAST (1)
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MDHM_YEAST (1)
YMY9_YEAST (1)
ARF1_YEAST (1)
IF4B_YEAST (1)
G3P2_YEAST (1)

CHEBI ID

CHEBI:46905 (1)
CHEBI:17752 (1)
CHEBI:30754 (1)
CHEBI:57589 (1)
CHEBI:16015 (1)
CHEBI:21949 (1)
CHEBI:70819 (1)
CHEBI:17191 (1)
CHEBI:17310 (1)
CHEBI:49033 (1)

Metabolite Name

N6-acetyl-L-lysine (1)
Quercetin 3-O-Xylosyl-Rutinoside (1)
4-Morpholinepropanesulfonic Acid (1)
Glucose Lactate Acetate (1)
1-(Tert-Butylamino)-3-(3-Fluorophenyl)Thiourea (1)
3,5-Dihydroxy-6-Methyl-2,3-Dihydro-4H-Pyran-4-One (1)
3-Methyl-2-Butenal (1)
2-Amino-9-[(4S)-4-Hydroxy-5-(Hydroxymethyl)Oxolan-2-Yl]-1H-Purin-6-One (1)
Feruloyl Allylamine (1)
Sulfometuron-Methyl (1)
Hydroxy Bosentan (1)
Monnieriside G (1)
Tetrahydropterin (1)
5-(3,4-Dimethoxyphenyl)-3,4-Dimethyloxolan-2-One (1)
1-[3-(4-Chlorophenoxy)Propyl]-2-Methyl-4-Nitroimidazole (1)
Feruloyl O-Methyldopamine (1)
7-Tert-Butyl-N-(Thiophen-2-Ylmethyl)Pyrazolo[1,5-A]Pyrimidine-5-Carboxamide (1)
7-O-Methyl Morroniside (1)
Erysenegalensein J (1)
Bornyl Ferulate (1)
Prostaglandin Pge2 1-Glyceryl Ester (1)
Kuwanon G (1)
N-Phenethyl-3-Phenyl-Acrylamide (1)
(9Z,12Z)-7,8,16-Trihydroxyoctadeca-9,12-Dienoic Acid (1)
(5Xi,6Beta,9Xi,13Xi,18Xi)-6-Hydroxy-3-Oxolup-20(29)-En-28-Oic Acid (1)
3,4-Dihydro-6,8-Dihydroxy-3-(10-Hydroxyundecyl)Isocoumarin (1)
Ganoderic Acid K (1)
3-O-P-Trans-Coumaroylalphitolic Acid (1)
Tyr-Val-Leu (1)
Ganoderic Acid Epsilon (1)

IsPrivate

False (1)

First Public Date

2024 (14)
2026 (13)
2025 (12)
2022 (6)
2023 (5)
2020 (5)
2021 (4)
2018 (4)
2014 (4)
2013 (4)
2015 (3)
2017 (2)
2016 (2)
2019 (1)

Classification

bacteria (10)
protozoa (1)

Modelling Approach

Ordinary differential equation model (1)

Study type

RNA-seq of coding RNA (164)
Transcription profiling by array (110)
ChIP-seq (31)
RNA-seq of coding RNA from single cells (17)
Animal - High-throughput sequencing (8)
Other (8)
Methylation profiling by high throughput sequencing (7)
RNA-seq of total RNA (7)
RNA-seq of non coding RNA (7)
Unknown experiment type (3)
ChIP-chip by tiling array (3)
High-throughput sequencing (3)
Cell line - High-throughput sequencing (3)
Comparative genomic hybridization by array (3)
Cell line - One-color microarray (2)
Ribo-seq (2)
PRO-seq (1)
MNase-seq (1)
Human - High-throughput sequencing (1)
ChIP-chip by array (1)
RIP-seq (1)
MicroRNA profiling by array (1)

Release Date

2014 (63)
2015 (57)
2013 (54)
2012 (41)
2021 (38)
2025 (37)
2016 (37)
2022 (35)
2010 (35)
2024 (30)
2023 (30)
2020 (29)
2026 (25)
2019 (25)
2011 (25)
2018 (21)
2017 (19)
2008 (16)
2009 (8)
2007 (6)
2006 (5)
2005 (4)
2004 (2)
2003 (2)
2002 (1)
2000 (1)

Lab affiliation

Department of Biology, University of Crete, Heraklion, Crete, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, GR70013, Heraklion, Crete, Greece (1)
Westlake University 600 Dunyu, Hangzhou Zhejiang, 310030, China (1)
Institut de recherches cliniques de Montréal, Center for Genetic and Neurological Diseases,Montréal, QC, Canada Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada Division of Experimental Medicine, McGill University, Montreal, QC, Canada (1)
Center for Genomics and Systems Biology Department of Biology New York University, New York, NY, 10003, USA (1)
Department of Biology - New York University Center for Genomics and Systems Biology New York, NY , USA (1)
Department of Microbiology and Immunology, Department of Biochemistry and Biophysics, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill (1)
Faculty of Biology, Technion Israel Institute of Technology (1)
Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, Hale Family Pancreatic Cancer Research Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA (1)
Université de Rennes-1, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, Equipe labelisée LNCC 2014, Rennes, France. (1)
Istituto di Genetica Molecolare CNR, Pavia 27100, Italy (1)
Department of Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany (1)
Cedars-Sinai Medical Center, Smidt Heart Institute (1)
Associate Professor of Chemistry, University of California, Riverside (1)
Lab PI (1)
Institute of Molecular Biology (IMB), Mainz, Germany (1)
Department of Biology, University of Konstanz, Germany (1)
Cedars-Sinai Medical Center (1)
Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany (1)
Associate Professor of Proteomics Departments of Chemistry and Biochemistry | University of Oxford (1)

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Protein UFMylation regulates ribosomal DNA double-stranded break repair

Ribosomal DNA (rDNA) arrays are highly repetitive regions of the genome which encode essential genes required to produce ribosomes. DNA double-stranded breaks (DSBs) generated within rDNA genes elicit a unique cellular response involving robust transcriptional silencing and nucleolar reorganization ...

ORGANISM(S): Homo sapiens (Human)

2024-09-16 | PXD048568 | Pride

SGP2024 - Apoptosis_AgNPs

This model explores the temporal dynamics of silver nanoparticles (AgNPs)-induced apoptosis using dynamic simulations in COPASI. It provides a time-resolved framework for understanding how cellular stress progresses to programmed cell death.

2025-09-08 | MODEL2412210001 | BioModels

Quantitative phosphoproteomic analysis of DNA-PK substrates

We conducted a TMT based phosphoproteomic analysis to identify DNA-PK substrates.

ORGANISM(S): Homo Sapiens

2023-01-15 | PXD039454 |

Protein UFMylation regulates ribosomal DNA double-stranded break repair

PRJNA1067156 | ENA

RNA-seq of mouse heart that is both heart SOD2 knockout and deficient for mitochondrial DNA repair

To study whether increase in mitochondrial oxidative stress (SOD2 removal) and decrease in mitochondrial DNA repair (Ogg1 dMTS) results into increase in mutations in mitochondrial RNA (mtRNA). Oxidative stress has been suggested to induce mutations in mtDNA and as DNA is used as a template in transc...

ORGANISM(S): Mus musculus

2018-07-13 | E-MTAB-6534 | biostudies-arrayexpress

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

Mechanistic insights in transcription-coupled nucleotide excision repair of ribosomal DNA.

Not available

S-EPMC6055190 | biostudies-literature

Synergistic targeting of DNA-PK and KIT signaling pathways in KIT mutant acute myeloid leukemia

Acute Myeloid Leukemia (AML) is the most common and aggressive form of acute leukemia, with a 5-year survival rate of just 24%. Over a third of all AML patients harbor activating mutations in kinases, such as the receptor tyrosine kinases FLT3 and KIT. FLT3 and KIT mutations are associated with poor...

ORGANISM(S): Mus Musculus

2023-01-26 | PXD030214 | panorama

C8orf33 dictates DNA double-strand break repair choice by modulating KAT8-mediated H4K16 acetylation

DNA double-strand breaks (DSBs) are repaired through distinct pathways, including homologous recombination (HR) and non-homologous end joining (NHEJ). The regulation of repair pathway choice is crucial for maintaining genomic stability and preventing carcinogenesis. Consequently, there is growing in...

ORGANISM(S): Homo sapiens (Human)

2025-10-29 | PXD062780 | Pride

Acetylation Dna double-strand break

Protein UFMylation regulates ribosomal DNA double-stranded break repair

ORGANISM(S): Homo sapiens

2024-01-29 | GSE253809 | GEO

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