Dna-bound proteins

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Transcriptomics (4773)
Genomics (2385)
Unknown (2286)
Proteomics (446)
Other (50)
Multiomics (28)
Metabolomics (14)
Methylation profiling (7)
Models (5)

Organisms

Homo sapiens (1648)
Mus musculus (1473)
Drosophila melanogaster (895)
Caenorhabditis elegans (524)
Arabidopsis thaliana (374)
Saccharomyces cerevisiae (329)
Rattus norvegicus (128)
Schizosaccharomyces pombe (122)
Escherichia coli (61)
Danio rerio (50)
Thermus thermophilus HB8 (39)
Mycobacterium tuberculosis (30)
Candida albicans (27)
synthetic construct (27)
Sus scrofa (26)
Bos taurus (25)
Salmo salar (23)
Sinorhizobium meliloti (21)
Gallus gallus (21)
Escherichia coli str. K-12 substr. MG1655 (21)
Zea mays (20)
Staphylococcus aureus (20)
Bacillus subtilis (17)
Streptomyces coelicolor A3(2) (16)
Streptomyces venezuelae (15)
Triticum aestivum (15)
Apis mellifera (14)
Oncorhynchus mykiss (14)
Salmonella enterica subsp. enterica serovar Typhimurium (12)
Macaca mulatta (11)

Organisms

Homo sapiens (124)
Mus musculus (81)
Saccharomyces cerevisiae (29)
Drosophila melanogaster (25)
Arabidopsis thaliana (22)
Schizosaccharomyces pombe (7)
Caenorhabditis elegans (5)
Escherichia coli (3)
Nomascus leucogenys (3)
synthetic construct (3)
human gammaherpesvirus 4 (2)
Candida albicans (2)
Pseudomonas aeruginosa (2)
Escherichia coli str. K-12 substr. MG1655 (2)
Orbilia oligospora (2)
Geobacter sulfurreducens (2)
Streptomyces coelicolor (2)
Streptomyces griseus (2)
Haloferax volcanii (2)
Bacillus subtilis (2)
Danio rerio (2)
Ascaris suum (1)
Escherichia coli str. K-12 substr. DH10B (1)
Escherichia coli BW25113 (1)
Streptococcus pyogenes (1)
Campylobacter jejuni (1)
Plasmodium falciparum (1)
Streptococcus pneumoniae (1)
Staphylococcus aureus (1)
Mnemiopsis leidyi (1)

Repository

biostudies-arrayexpress (6564)
ENA (415)
geo (273)
pride (268)
MassIVE (93)
jPOST (26)
LINCS (26)
MetaboLights (14)
iProX (13)
EGA (11)
PanoramaPublic (10)
BioModels (5)
GPMDB (2)
PAXDB (2)

Tissue

Cell culture (81)
Epithelial cell (24)
Embryonic stem cell (16)
Permanent cell line cell (15)
Cell suspension culture (8)
Brain (8)
B cell (7)
Kidney (7)
Fibroblast (6)
Blood cell (6)
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Embryo (5)
Early embryonic cell (4)
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Type II pneumocyte (3)
HEK-293T cell (3)
Pluripotent stem cell (3)
HeLa cell (3)
Skin (3)
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Colon (3)
Lung (3)
Blood plasma (3)
Leaf (3)
Microvascular endothelial cell (2)
Prokaryotic cell (2)
Gametocyte (2)
Photosynthetic cell (2)
Melanocyte (2)

Disease

Normal (32)
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Adenocarcinoma (3)
Neuroblastoma (3)
Squamous Cell Carcinoma (2)
Breast adenocarcinoma (2)
Chronic myeloid leukemia (2)
Chronic lymphocytic leukemia (2)
Cancer (2)
Mammary tumor (2)
Lung cancer (2)
Multiple myeloma (2)
Retinoblastoma (1)
Chronic lymphoid leukemia (1)
Amyotrophic lateral sclerosis (1)
Arrhythmias and right ventricular dysfunction (1)
HIV encephalitis (1)
SMARD1 (1)
B-precursor acute lymphoblastic leukemia (1)
Burn injury (1)
Measles virus infected (1)
Diabetes mellitus type 1 (1)
Inflammatory bowel disease (1)
Dermal neurofibroma (1)
Hepatomegaly (1)
Chronic lymphocytic leukemia (CLL) (1)

Technology Type

Mass Spectrometry (268)
Shotgun proteomics (105)
Affinity purification coupled with mass spectrometry proteomics (104)
Bottom-up proteomics (55)
Data-dependent acquisition (33)
KINOMEscan (23)
Fluorescence intensity (23)
Chemical cross-linking coupled with mass spectrometry proteomics (22)
Data-independent acquisition (12)
Gel-based experiment (11)
Mass spectrometry (8)
Top-down proteomics (6)
SWATH MS (6)
Mass spectrometry assay (5)
ELISA (3)
Chemiluminescence (3)
Affinity proteomics (2)
MSE (2)
DiaPASEF (2)
All-ion fragmentation (2)
Illumina HiSeq 2000 (1)
NMR spectroscopy (1)
SomaScan affinity proteomics (1)
Olink affinity proteomics (1)
Proteogenomics (1)
Mass spectrometry imaging (1)
HDMSE (1)
SRM/MRM (1)

Instrument Platform

Illumina HiSeq 2000 (103)
NextSeq 500 (97)
Illumina HiSeq 2500 (82)
Illumina NovaSeq 6000 (72)
Illumina HiSeq 4000 (65)
Illumina MiSeq (37)
NextSeq 550 (21)
Illumina Genome Analyzer II (19)
Axon GenePix 4000B scanning hardware (19)
Illumina Genome Analyzer IIx (18)
Illumina HiSeq 1500 (15)
Axon- GenePix4000B (10)
418 [Affymetrix] (10)
Scanning hardware (10)
NextSeq 2000 (10)
GenePix 4000B [Axon Instruments] (8)
Illumina HiSeq 3000 (8)
G2565BA DNA microarray scanner [Agilent] (7)
ScanArray Express HT [PerkinElmer] (7)
Illumina NovaSeq X (7)
Axon GenePix 4000A scanning hardware (6)
AB SOLiD 4 System (6)
GenePix 4000A [Axon Instruments] (5)
Variable Atmosphere Incubator (5)
ScanArray 4000 [PerkinElmer] (4)
ScanArray Lite [PerkinElmer] (4)
NanoDrop (4)
ScanArray 4000XL [PerkinElmer] (4)
Vortex (4)
Illumina HiSeq 1000 (4)

Publication Date

2013 (1203)
2010 (888)
2011 (817)
2014 (625)
2015 (603)
2012 (587)
2016 (403)
2008 (286)
2009 (244)
2007 (196)
2021 (158)
2023 (156)
2022 (138)
2024 (125)
2004 (119)
2025 (110)
2020 (97)
2019 (94)
2018 (94)
2006 (88)
2026 (84)
2005 (82)
2017 (77)
2003 (10)
2002 (1)
2001 (1)

UNIPROT ID/AC

IGSF2_MOUSE (1)
TMM52_MOUSE (1)
MCIN_MOUSE (1)
ELF5_MOUSE (1)
IL12A_MOUSE (1)
CXA10_MOUSE (1)
E9Q6B9_MOUSE (1)
MRGB2_MOUSE (1)
TSCOT_MOUSE (1)
LRRC9_MOUSE (1)
A2CF17_MOUSE (1)
PRDM5_MOUSE (1)
SPB11_MOUSE (1)
10090.ENSMUSP00000137545 (1)
GDPD3_MOUSE (1)
CCNQ_MOUSE (1)
PATE2_MOUSE (1)
OL473_MOUSE (1)
M4A6C_MOUSE (1)
SLNL1_MOUSE (1)
E9PWJ8_MOUSE (1)
GP174_MOUSE (1)
S13A2_MOUSE (1)
ZN664_MOUSE (1)
SATL1_MOUSE (1)
S26A5_MOUSE (1)
Q99N04_MOUSE (1)
PTHD3_MOUSE (1)
TR135_MOUSE (1)
SOCS3_MOUSE (1)

CHEBI ID

CHEBI:17596 (4)
CHEBI:17287 (3)
CHEBI:18012 (3)
CHEBI:15354 (3)
CHEBI:16919 (3)
CHEBI:16737 (3)
CHEBI:16708 (3)
CHEBI:16015 (3)
CHEBI:16108 (3)
CHEBI:16856 (3)
CHEBI:17858 (3)
CHEBI:15428 (3)
CHEBI:15891 (3)
CHEBI:17724 (3)
CHEBI:30769 (3)
CHEBI:15741 (3)
CHEBI:28044 (3)
CHEBI:16335 (3)
CHEBI:16057 (2)
CHEBI:15811 (2)
CHEBI:9532 (2)
CHEBI:35584 (2)
CHEBI:17797 (2)
CHEBI:16349 (2)
CHEBI:17266 (2)
CHEBI:17553 (2)
CHEBI:17066 (2)
CHEBI:15422 (2)
CHEBI:70959 (2)
CHEBI:18139 (2)

Metabolite Name

Choline (8)
Adenosine (8)
L-Arginine (7)
L-Tyrosine (7)
Taurine (7)
Guanosine (7)
Inosine (7)
Picolinic acid (6)
L-Carnitine (6)
Creatine (6)
Pantothenic acid (6)
Creatinine (6)
Guanine (6)
Myristic acid (6)
Adenine (6)
Uridine (6)
O-Phosphoethanolamine (5)
1,2,3-Trihydroxybenzene (5)
Mannitol (5)
Glutathione (5)
L-Aspartic acid (5)
L-Proline (5)
L-Alanine (5)
Adenosine monophosphate (5)
L-Tryptophan (5)
S-Adenosylmethionine (5)
Hypoxanthine (5)
1-Methyladenosine (5)
Uracil (5)
Malic acid (5)

First Public Date

2014 (57)
2025 (42)
2024 (34)
2023 (34)
2026 (31)
2022 (29)
2021 (29)
2017 (29)
2015 (29)
2013 (27)
2018 (22)
2020 (20)
2019 (16)
2016 (14)
2011 (2)

Modelling Approach

Ordinary differential equation model (5)

Lab affiliation

DZNE Munich, Neuroproteomics, Feodor-Lynen Str. 17, 81377 Munich, Germany (5)
Medical Research Council Senior Research Fellow Associate Professor in RNA Biochemistry and Research Group Leader Centre for Synthetic and Systems Biology (SynthSys) University of Edinburgh Max Born Crescent CH Waddington Building, room 3.06 EH9 3BF Edinburgh UK (4)
Max Planck Institute of Immunobiology and Epigenetics Proteomics Unit Stuebeweg 51 79108 Freiburg Germany (4)
Thoracic Oncology Molecular Medicine Program Moffitt Cancer Center Tampa, FL, USA (4)
Medical Research Council Mitochondrial Biology Unit, University of Cambridge. U.K. (4)
Molecular Leukemogenesis Group, German Cancer Research Center, Heidelberg, Germany Heidelberg University, Medical Faculty, Heidelberg, Germany, 6Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany (3)
Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany (3)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (3)
University of Geneva, Faculty of Medicine, Geneva, Switzerland (2)
Director, Centre for Proteome Research Department of Biochemistry & Systems Biology Institute of Systems, Molecular & Integrative Biology University of Liverpool Crown Street, Liverpool L69 7ZB +44 151 795 4424 (2)
1. Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel 2. Computer Science Department, Technion - Israel Institute of Technology, Haifa 320003, Israel (2)
Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians University, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany (2)
Centre for Gene Regulation and Expression School of Life Sciences, University of Dundee, Dundee (2)
Chair, Quantitative Proteomics Director, Proteome Center Tuebingen Interfaculty Institute for Cell Biology University of Tuebingen Auf der Morgenstelle 15 72076 Tuebingen Germany (2)
Department of Chemistry, University of California Riverside (2)
Dept. of Molecular Biosciences, University of Texas at Austin, Texas 78712 USA (2)
Institute of Molecular Biology (IMB), Mainz, Germany (2)
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 (2)
The Institute of Cancer Research (2)
Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands (2)
Institute of Molecular Biology (IMB) (2)
Head of the Curie Institute Mass Spectrometry Platform (2)
University of Edinburgh (2)
Harvard Medical School Department of Neurobiology (1)
Distinguished Professor, University of California Riverside (1)
Laboratory of Molecular Biology, Intercollegiate Faculty of Biotechnology UG&MUG (1)
Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Belgium (1)
Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (1)
Department of Molecular Microbiology & Immunology Oregon Health & Science University 3181 SW Sam Jackson Park Road Portland, Oregon 97239, USA (1)
Max-Planck of Biochemistry, Experimental Systems Immunology Germany (1)

IsPrivate

False (5)

Classification

bacteria (13)
fungi (2)
viruses (2)
helminths (1)
protozoa (1)

Modification

N6 (2)
N6-dimethyl-L-lysine (1)
2x(15)N labeled L-lysine (1)
Not available (1)
4x(15)N labeled L-arginine (1)

Study type

Transcription profiling by array (2375)
ChIP-seq (1741)
ChIP-chip by tiling array (861)
RNA-seq of coding RNA (557)
ChIP-chip by array (179)
Other (146)
RNA-seq of non coding RNA (82)
Unknown experiment type (80)
Methylation profiling by array (70)
Comparative genomic hybridization by array (69)
Methylation profiling by high throughput sequencing (57)
Proteomic profiling by array (33)
Transcription profiling by tiling array (25)
CLIP-seq (23)
Cell line - High-throughput sequencing (22)
RIP-seq (22)
DNA-seq (22)
Animal - High-throughput sequencing (21)
RNA-seq of coding RNA from single cells (21)
MicroRNA profiling by array (16)
High-throughput sequencing (14)
RNAi profiling by array (12)
RNA-seq of total RNA (12)
Transcription profiling by SAGE (7)
CUT&RUN (7)
Animal - One-color microarray (6)
Transcription profiling by RT-PCR (6)
Hi-C (6)
Human - High-throughput sequencing (5)
Translation profiling (5)

Release Date

2013 (1291)
2010 (958)
2011 (918)
2014 (729)
2015 (688)
2012 (684)
2016 (464)
2008 (337)
2009 (335)
2007 (237)
2021 (234)
2022 (210)
2023 (199)
2018 (189)
2020 (180)
2019 (178)
2024 (165)
2025 (153)
2017 (152)
2004 (138)
2006 (122)
2005 (119)
2003 (37)
2026 (36)
2002 (22)
1998 (22)
2000 (20)
2001 (18)
1999 (9)
1997 (5)

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Human proteins bound to RNA/DNA hybrid

PRJNA482858 | ENA

Genome-wide binding of replication initiation proteins in Bacillus subtilis

Initiation of DNA replication requires binding of the initiator protein, DnaA, to specific binding sites in the chromosomal origin of replication, oriC. In low G+C Gram-positive bacteria, the primosomal proteins DnaD and DnaB, in conjunction with loader ATPase DnaI, load the replicative helicase at ...

ORGANISM(S): Bacillus subtilis

2010-12-07 | E-GEOD-23686 | biostudies-arrayexpress

Sequence, Biogenesis, and Function of Diverse sRNA Classes Bound to the Piwi-family Proteins of Tetrahymena thermophila

PAZ/PIWI-domain (PPD) proteins carrying small RNAs (sRNAs) function in gene and genome regulation. The ciliate Tetrahymena thermophila encodes numerous PPD proteins exclusively of the Piwi clade. We show that the three Tetrahymena Piwi-family proteins (Twis) preferentially expressed in growing cells...

ORGANISM(S): Tetrahymena thermophila

2009-11-23 | E-GEOD-17006 | biostudies-arrayexpress

Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

This SuperSeries is composed of the following subset Series: GSE3968: Puf proteins, RNA co-immunopurification GSE3969: Puf3delta vs. wild type comparison Abstract: Genes encoding RNA-binding proteins are diverse and abundant in eukaryotic genomes. Although some have been shown to have roles in post...

ORGANISM(S): Saccharomyces cerevisiae

2006-03-07 | E-GEOD-4393 | biostudies-arrayexpress

Stochastic ratchet mechanisms for replacement of proteins bound to DNA.

Not available

S-EPMC4131839 | biostudies-literature

Computational structural analysis: multiple proteins bound to DNA.

Not available

S-EPMC2532747 | biostudies-literature

Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues

Tissue lysis using urea buffer was adopted in our previously published CPTAC protocol for mass spectrometry (MS)-based quantitative global proteomic and phosphoproteomic analysis. Herein, we reported an update to this initial protocol by implementing a sonication step into urea-based tissue lysis. S...

ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse)

2025-07-28 | PXD050336 | Pride

Polycomb proteins remain bound to chromatin and DNA during DNA replication in vitro.

Not available

S-EPMC2667909 | biostudies-literature

Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations.

Not available

S-EPMC3789251 | biostudies-literature

Isolation of Proteins on Chromatin Reveals Signaling Pathway-Dependent Alterations in the DNA-Bound Proteome.

Not available

S-EPMC11889358 | biostudies-literature

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