Repair synthesis

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Technology Type

Mass Spectrometry (90)
Shotgun proteomics (41)
Affinity purification coupled with mass spectrometry proteomics (25)
Bottom-up proteomics (18)
Data-dependent acquisition (8)
Gel-based experiment (7)
Mass spectrometry (6)
Mass spectrometry assay (5)
SWATH MS (5)
Data-independent acquisition (4)
ILLUMINA, Illumina HiSeq 2500 (1)
Illumina HiSeq 2000 (1)
NMR spectroscopy (1)
Affinity proteomics (1)
MSE (1)
All-ion fragmentation (1)
HDMSE (1)
SRM/MRM (1)
Top-down proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (91)
Illumina HiSeq 2000 (47)
BGISEQ-500 (30)
Illumina HiSeq 2500 (26)
Illumina HiSeq 4000 (22)
Illumina NovaSeq X (17)
NextSeq 500 (15)
Illumina MiSeq (11)
NextSeq 550 (11)
DNBSEQ-G400 (9)
DNBSEQ-T7 (9)
Illumina Genome Analyzer IIx (6)
Illumina Genome Analyzer II (4)
Illumina (4)
NextSeq 2000 (3)
Illumina HiSeq 1000 (3)
HiSeq X Ten (3)
Illumina HiSeq 1500 (3)
Single cells were captured using the 10x Genomics Chromium Controller. (2)
Illumina HiScanSQ (2)
BAS-5000 [FUJIFILM] (2)
NA (2)
Illumina HiSeq X (2)
N/A (2)
MinION (2)
Cell Ranger (1)
Computational analysis using R (Seurat v5.0.0) (1)
Qubit 4 Fluorometer (1)
Qsep400 (1)
Qubit fluorometer (1)

Publication Date

2015 (170)
2013 (164)
2014 (142)
2012 (125)
2025 (114)
2026 (108)
2016 (100)
2011 (85)
2010 (83)
2023 (82)
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2020 (57)
2008 (51)
2009 (41)
2017 (37)
2019 (31)
2018 (31)
2007 (27)
2006 (20)
2005 (12)
2004 (3)

CHEBI ID

CHEBI:16856 (2)
CHEBI:17858 (2)
CHEBI:28013 (2)
CHEBI:17111 (2)
CHEBI:15721 (2)
CHEBI:18009 (2)
CHEBI:16938 (2)
CHEBI:16001 (2)
CHEBI:25107 (1)
CHEBI:17720 (1)
CHEBI:42111 (1)
CHEBI:36080 (1)
CHEBI:18420 (1)
CHEBI:16897 (1)
CHEBI:16541 (1)
CHEBI:32816 (1)
CHEBI:16084 (1)
CHEBI:35780 (1)
CHEBI:29052 (1)
CHEBI:16027 (1)
CHEBI:16332 (1)
CHEBI:17797 (1)
CHEBI:17363 (1)
CHEBI:15361 (1)
CHEBI:17835 (1)
CHEBI:17794 (1)
CHEBI:17665 (1)
CHEBI:15422 (1)
CHEBI:16761 (1)
CHEBI:16908 (1)

Metabolite Name

Guanosine (5)
Adenosine (4)
Adenine (4)
Inosine (4)
Apixaban (3)
Janthitrem C (3)
Pyroglutamic acid (3)
Daidzin (3)
Nodularin (3)
L-Threonine (3)
Riboflavin (3)
Uric acid (3)
L-Leucine (3)
L-Tyrosine (3)
Hypoxanthine (3)
Met Glu Met (2)
UDP-xylose (2)
N-Acetyl-L-Leucine (2)
(-)-Corey Lactone Diol (2)
Desethylamiodarone (2)
Nitrogen mustard N-oxide (2)
GlcNAc1-3Gal1-4GlcNAcSp (2)
[(2S,3S,4S,5R,6R)-6-[(2S)-2,3-Di(octadecanoyloxy)propoxy]-3,4,5-trihydroxyoxan-2-yl]methanesulfonic acid (2)
Taxuspine Z (2)
Disulfoton sulfone (2)
Mycolactone E (2)
Phe4Cl-Thr-OH (2)
(3-{8-[5,7-dihydroxy-2-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-3-yl]-5,7-dihydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-2-yl}phenyl)oxidanesulfonic acid (2)
Mn(III)TBAP (2)
2,3,4,7,8,9,15,21,22,23,28-undecahydroxy-14-(hydroxymethyl)-13,25,32,35-tetraoxaoctacyclo[14.13.3.3(1),(2).0,(3).0,(1)(1).0(1),(2).0(1),(2).0(2),(3)(3)]pentatriaconta-1,3,5(30),6,8,10,19,21,23-nonaene-12,27,31,34-tetrone (2)

First Public Date

2025 (77)
2026 (59)
2014 (59)
2024 (58)
2023 (47)
2022 (43)
2021 (34)
2020 (27)
2019 (24)
2018 (20)
2017 (18)
2015 (14)
2016 (13)
2013 (9)

Modelling Approach

Ordinary differential equation model (2)

Study status

Completed (1)

Lab affiliation

Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (4)
Medical Oncology and Pulmonology, University Hospital Tübingen, Germany (3)
Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany (2)
Burns and Trauma Research,School of Biomedical Sciences, Queensland University of Technology (2)
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, United States (2)
Applied Science and Technology Department–BioSolar Lab, Politecnico di Torino,Italy (1)
Department of Human Genetics, Leiden University Medical Center, The Netherlands (1)
Department of Genetics and Development Herbert Irving Comprehensive Cancer Center Columbia University Irving Medical Center New York, NY, USA (1)
Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands (1)
Adolf Butenandt Institute Schillerstrasse 44 80336 Munich (1)
Vascular Dysfunction Department European Center for Angioscience Medical Faculty Mannheim Heidelberg University (1)
Director of ARC center in PlantEnergy Bilology at School of Molcular Science at Univerity of Western Australia (1)
Biomedical Research Center, Slovak Academy of Sciences (1)
Molecular Genetics TU Kaiserslautern Germany (1)
Biomedical Sciences Research Center 'Alexander Fleming' 34 Fleming St., 16672, Vari, Greece. (1)
6Department of Biochemistry, College of Medicine, Hallym University, Chuncheon 24252, Gangwon-do, Republic of Korea (1)
Roderick O’Sullivan Ph.D., Dept. Pharmacology & Chemical Biology, University of Pittsburgh, UPMC Hillman Cancer Center, 5115 Centre Avenue Pittsburgh, PA 15213, USA (1)
Netherlands Cancer Institute, Amsterdam, Netherlands. (1)
functionla proteomics, ICR (1)
Space Biochemistry Group, Department of Biophysical Chemistry, University of Vienna, Vienna, Austria (1)
Department of Cancer Research and Molecular Medicine Faculty of Medicine Laboratory Centre, 5th floor. Erling Skjalgssons gt. 1 Norwegian University of Science and Technology NTNU 7006 Trondheim, Norway Tel: +47 72573076; Fax: +47 72576400 Cell. phone: +47 91825455 (1)
Renmin South Rd. 4-13, Chengdu 610041, China (1)
Molecular Proteomics Laboratory, Biological Medical Research Center, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany (1)
Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin 150040, China (1)
Biochemistry Centre Regensburg (BCR), Universität Regensburg, 93053 Regensburg, Germany (1)
Andalusian Center for Molecular Biology and Regenerative medicine, CABIMER-US (1)
Max Planck Unit for the Science of Pathogens, Chariteplatz 1, 10117 Berlin, Germany (1)
Lung Repair & Regeneration Department, Boehringer Ingelheim Pharma GmbH & Co. KG (1)
Department of Cell Biology, Center of Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), Av. Instituto Politécnico Nacional 2508, CP 07360 Ciudad de México (CDMX), México. Tel.: +52 55 5747 3354 (1)
Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, Key Laboratory of Animal Nutrition and Feed Science, Jilin Province, College of Animal Science and Technology, Jilin Agricultural University, Changchun, P. R. China 130118 (1)

Keyword

Levocetirizine (1)
Capecitabine (1)
Bevacizumab (1)

IsPrivate

False (2)

Classification

bacteria (28)
fungi (3)
helminths (1)
protozoa (1)

Modification

2x(15)N labeled L-lysine (2)
4x(15)N labeled L-arginine (2)
Not available (1)

Study type

RNA-seq of coding RNA (504)
Transcription profiling by array (475)
ChIP-seq (82)
Other (29)
Methylation profiling by high throughput sequencing (27)
RNA-seq of coding RNA from single cells (23)
RNA-seq of total RNA (15)
Animal - High-throughput sequencing (12)
Unknown experiment type (11)
Comparative genomic hybridization by array (9)
DNA-seq (8)
Cell line - High-throughput sequencing (6)
ChIP-chip by tiling array (5)
Human - High-throughput sequencing (5)
RNA-seq of non coding RNA (5)
Methylation profiling by array (4)
High-throughput sequencing (3)
ChIP-chip by array (3)
Plant - High-throughput sequencing (2)
Cell line - One-color microarray (2)
Transcription profiling by RT-PCR (2)
Hi-C (2)
GRO-seq (1)
Transcription profiling by SAGE (1)
MNase-seq (1)
RNA-seq of non coding RNA from single cells (1)
One-color microarray (1)
Human - Single-cell sequencing (1)
Transcription profiling by tiling array (1)
Genotyping by array (1)

Release Date

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2013 (249)
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2014 (243)
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2020 (237)
2016 (213)
2012 (204)
2017 (174)
2019 (167)
2018 (150)
2011 (147)
2010 (143)
2009 (104)
2026 (102)
2008 (95)
2007 (49)
2006 (37)
2005 (24)
2004 (24)
2003 (10)
2001 (9)
2002 (6)
2000 (5)
1999 (4)
1998 (1)

Location

United States (1)

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DNA repair and recovery of RNA synthesis following exposure to ultraviolet light are delayed in long genes

The kinetics of DNA repair and RNA synthesis recovery in human cells following UV-irradiation were assessed using nascent RNA Bru-seq and quantitative long PCR. It was found that UV light inhibited transcription elongation and that recovery of RNA synthesis occurred as a wave in the 5’-3’ direction ...

ORGANISM(S): Homo sapiens

2015-03-03 | E-GEOD-65985 | biostudies-arrayexpress

RecG Directs DNA Synthesis During Double-Strand Break Repair [ChIP-seq]

In the bacterium Escherichia coli, RecG directs DNA synthesis during the repair of DNA double-strand breaks by homologous recombination. Examination of RecA binding during double-strand break repair in Escherichia coli in the presence and absence of RecG protein

ORGANISM(S): Escherichia coli

2016-05-19 | E-GEOD-77181 | biostudies-arrayexpress

RecG Directs DNA Synthesis During Double-Strand Break Repair [Chromosomal marker frequency analysis]

In the bacterium Escherichia coli, RecG directs DNA synthesis during the repair of DNA double-strand breaks by homologous recombination. Chromosomal marker frequency analysis (MFA) following induction of a DSB in the absence and presence of RecG

ORGANISM(S): Escherichia coli

2016-05-19 | E-GEOD-77183 | biostudies-arrayexpress

CPD-seq mapping of UV damage formation and repair in yeast

UV-induced DNA lesions are an important contributor to mutagenesis and cancer, but it is not fully understood how the chromosomal landscape influences UV lesion formation and repair. We have used a novel high-throughput sequencing method to precisely map UV-induced cyclobutane pyrimidine dimers (CPD...

ORGANISM(S): Saccharomyces cerevisiae

2016-08-19 | E-GEOD-79977 | biostudies-arrayexpress

Roles for the Transcription Elongation Factor NusA in Both DNA Repair and Damage Tolerance Pathways in Escherichia coli

Here we report our observations that have led us to propose that the transcription elongation factor NusA promotes a novel class of transcription-coupled repair (TCR) in addition to its previously proposed role in recruiting translesion synthesis (TLS) DNA polymerases to gaps encountered during tran...

ORGANISM(S): Escherichia coli

2010-07-14 | E-GEOD-22829 | biostudies-arrayexpress

RecG Directs DNA Synthesis During Double-Strand Break Repair

This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Escherichia coli

2016-05-19 | E-GEOD-77184 | biostudies-arrayexpress

The Anticancer Mechanism of the Ribonucleotide Reductase Inhibiting Drug COH29 Involves Suppression of DNA Repair

Mechanism of Action Study for COH29 Compare COH29 treatment in DNA-repair deficient cell line with truncated BRCA1 (HCC1937) versus phenotypically normal cell line with exogenous WT BRCA1 expression (HCC1937+BRCA1)

ORGANISM(S): Homo sapiens

2015-05-08 | E-GEOD-55004 | biostudies-arrayexpress

Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links part 2 of 2: AP-MS DATA (QUBIC)

DNA interstrand crosslinks (ICLs) block replication fork progression by inhibiting DNA strand separation. Repair of ICLs requires sequential incisions, translesion DNA synthesis, and homologous recombination, but the full set of factors involved in these transactions remains unknown. Here we establi...

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

2016-03-13 | MSV000079577 | MassIVE

Precision genome editing using synthesis-dependent repair of Cas9-induced DNA breaks

PRJNA420568 | ENA

Expression data from SKOV3 cells treated with SAHA or vehicle control

We performed a microarray experiment to assess SAHA-induced changes in expression of genes of the homologous recombination DNA repair pathway SKOV-3 ovarian cancer cells were treated with 1ÂµM SAHA or vehicle-control (0.01% DMSO) for 6 or 24 hours, harvested and processed for RNA isolation. Data fo...

ORGANISM(S): Homo sapiens

2014-03-19 | E-GEOD-53603 | biostudies-arrayexpress

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