u1 - OmicsDI

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Unknown (692)
Transcriptomics (394)
Genomics (391)
Proteomics (67)
Other (40)
Models (3)
Metabolomics (2)
Genomic (1)
Methylation profiling (1)
Multiomics (1)

Organisms

Homo sapiens (287)
Mus musculus (123)
Saccharomyces cerevisiae (51)
Arabidopsis thaliana (25)
Drosophila melanogaster (23)
Caenorhabditis elegans (11)
Schizosaccharomyces pombe (6)
Human adenovirus 2 (6)
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Rattus norvegicus (4)
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synthetic construct (2)
Trypanosoma brucei (2)
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Beauveria bassiana ARSEF 2860 (1)
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Oryctolagus cuniculus (1)

Organisms

Homo sapiens (115)
Mus musculus (37)
Panicum virgatum (30)
Saccharomyces cerevisiae (8)
Drosophila melanogaster (6)
Human adenovirus 2 (5)
Agaricus bisporus U1 (4)
Saccharolobus solfataricus (4)
Schizosaccharomyces pombe (4)
Arabidopsis thaliana (4)
Salicornia virginica (3)
Dyadobacter pollutisoli (2)
Escherichia coli (2)
Aquimarina sp. U1-2 (1)
Escherichia coli O5 str. U1-41 (1)
Streptomyces sp. MMS24-U1 (1)
Escherichia coli O5:K4(L):H4 str. ATCC 23502 (1)
Viridibacillus arvi (1)
Cuscuta campestris (1)
Acidovorax sp. (1)
Trypanosoma brucei (1)
Aspergillus luchuensis (1)
Caenorhabditis elegans (1)
Saccharomyces cerevisiae BY4741 (1)
Staphylococcus aureus (1)
Danio rerio (1)
Rattus norvegicus (1)
microbial mat metagenome (1)
synthetic construct (1)

Repository

biostudies-arrayexpress (331)
ENA (288)
geo (189)
pride (28)
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Tissue

Cell culture (5)
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Cell suspension culture (1)
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Primary cell (1)
Sciatic nerve (1)

Disease

Alzheimer's disease (2)
Colon cancer (2)
N/a (1)
Disease by infectious agent (1)
Human immunodeficiency virus infectious disease (1)
Parkinson's disease (1)

Technology Type

Mass Spectrometry (28)
Shotgun proteomics (15)
Affinity purification coupled with mass spectrometry proteomics (11)
Chemical cross-linking coupled with mass spectrometry proteomics (6)
Bottom-up proteomics (4)
Illumina HiSeq 2000 (2)
Illumina HiSeq 2000, Illumina Genome Analyzer IIx (1)
NMR spectroscopy (1)
Mass spectrometry assay (1)
Data-dependent acquisition (1)
HDMSE (1)
SRM/MRM (1)

Instrument Platform

Illumina HiSeq 2000 (8)
Illumina NovaSeq 6000 (5)
NextSeq 500 (5)
LTQ (5)
Orbitrap Fusion Lumos (5)
Illumina Genome Analyzer IIx (4)
Q Exactive Plus (4)
Illumina HiSeq 2500 (3)
Orbitrap Fusion (3)
TimsTOF Pro (3)
Ion Torrent Proton (2)
Illumina HiSeq 1500 (2)
NextSeq 550 (2)
Illumina HiSeq 4000 (2)
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Q Exactive (2)
Q Exactive HF (2)
Illumina Dragen RNAseq pipeline (1)
GenePix 4200A (1)
ScanArray [PerkinElmer] (1)
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Illumina Genome Analyzer II (1)
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Illumina NovaSeq X (1)
N/A (1)
NextSeq 2000 (1)
DNBSEQ-G400 (1)
MinION (1)
Illumina MiSeq (1)
Illumina HiSeq 3000 (1)

Publication Date

2013 (59)
2014 (48)
2016 (44)
2015 (43)
2023 (43)
2022 (39)
2011 (39)
2025 (35)
2012 (34)
2024 (31)
2020 (29)
2010 (27)
2021 (23)
2018 (18)
2019 (15)
2017 (13)
2026 (12)
2008 (11)
2009 (9)
2005 (7)
2007 (4)
2004 (2)
2006 (1)

UNIPROT ID/AC

Q8IZH2 (1)
Q96RS0 (1)
P62306 (1)
P62304 (1)
P62308 (1)
P62318 (1)
P62314 (1)
P14678 (1)
P62316 (1)
O14744 (1)
P52297 (1)
Q14974 (1)
P52292 (1)
Q16637 (1)
P43487 (1)
Q92973 (1)
Q9H814 (1)
O95149 (1)
O14980 (1)
P52298 (1)
Q09161 (1)
P08621 (1)
P09012 (1)
P09234 (1)
P60510 (1)
P62826 (1)
A0A024R8H9 (1)
A0A024RC46 (1)
A0A087WTX5 (1)
A0A087WVW2 (1)

ENSEMBL ID

ENSG00000170477 (1)
ENSG00000229353 (1)

CHEBI ID

CHEBI:74035 (1)
CHEBI:84596 (1)
CHEBI:37565 (1)
CHEBI:58189 (1)
CHEBI:43474 (1)
CHEBI:15422 (1)
CHEBI:132318 (1)
CHEBI:132317 (1)
CHEBI:37054 (1)
CHEBI:15740 (1)
CHEBI:24996 (1)
CHEBI:30089 (1)
CHEBI:18139 (1)
CHEBI:16947 (1)
CHEBI:16810 (1)
CHEBI:42191 (1)
CHEBI:17925 (1)
CHEBI:29987 (1)
CHEBI:15903 (1)
CHEBI:25094 (1)
CHEBI:18186 (1)
CHEBI:17790 (1)
CHEBI:17170 (1)
CHEBI:15347 (1)
CHEBI:24898 (1)
CHEBI:25017 (1)
CHEBI:15428 (1)
CHEBI:17268 (1)
CHEBI:27266 (1)
CHEBI:17750 (1)

Metabolite Name

M444T269 (1)
M263T196 (1)
M602T255 (1)
M337T253 (1)
M259T143 (1)
M299T175 (1)
M582T266 (1)
M283T274 (1)
M361T213 (1)
M353T239 (1)
5-(Trifluoromethyl)-1,3-thiazole-4-carboxylic acid (1)
2-Deoxyribose_1-phosphate (1)
(S)-2-Amino-7-phosphonoheptanoic acid (1)
2-Methoxy-4-nitrobenzoic acid (1)
N-Benzoyl-N'-(2-pyridinyl)thiourea (1)
3-Bromo-4-butoxybenzoic acid (1)
N-Phenyl-N'-(3-pyridinylmethyl)thiourea (1)
6-Fluoro-1H-indole-2,3-dione (1)
3-Chloro-5-fluoro-4-methoxybenzoic acid (1)
2-(2,5-Dioxohexahydroimidazo[4,5-d]imidazol-1(2H)-yl)-4-(methylsulfanyl)butanoic acid (1)
4-Oxazolecarboxylic acid (1)
4-(2-Naphthylamino)-4-oxobutanoic acid (1)
3-(4-Bromo-1H-pyrazol-1-yl)-2-methylpropanoic acid (1)
3-[(Methylsulfonyl)amino]-2-thiophenecarboxylic acid (1)
Fenoxaprop-P (1)
4,6-Dichloro-1H-indole-2-carboxylic acid (1)
4-Cyano-N-ethylbenzene-1-sulfonamide (1)
5-[(7-Chloro-4-quinolinyl)amino]-2-hydroxybenzoic acid (1)
5,6,7,8-Tetrahydro-1H-spiro[benzo[4,5]thieno[2,3-d]pyrimidine-2,1'-cyclohexane]-4(3H)-thione (1)
N,1-Diethyl-2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamide (1)

First Public Date

2023 (41)
2025 (39)
2017 (37)
2024 (27)
2022 (23)
2021 (19)
2019 (19)
2026 (18)
2020 (15)
2018 (15)
2014 (15)
2016 (8)
2015 (6)
2013 (5)
2012 (1)

Modelling Approach

Ordinary differential equation model (2)
Petri net (1)

Lab affiliation

ETH Zurich, Institute of Molecular Systems Biology (4)
Emory University School of Medicine Departments of Biochemistry and Neurology (2)
Associate Professor, Division of Hematology, Department of Internal Medicine, The Ohio State University Wexner Medical Center (1)
Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, USA (1)
Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747 Garching b. München (1)
Centre for Blood Research ; Oral & Biomedical Sciences University of British Columbia Canada (1)
Centre for Cancer Cell & Molecular Biology Barts Cancer Institute Queen Mary University of London Charterhouse Square London EC1M 6BQ U.K. (1)
Departamento de Bioquimica, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, SP, Brazil (1)
Department of Biochemistry, Emory University, Atlanta, GA, USA Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA (1)
Department of Chemistry and Biochemistry, University of California San Diego (1)
Department of Microbiology & Molecular Genetics University of California, Irvine Irvine, California, 92697 USA (1)
Department of Plant Biotechnology and Bioinformatics, Oxidative Stress Signaling Lab, Ghent University (1)
Departments of Molecular Neuroscience and Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel (1)
Division of Chemistry I, Department of Medical Biochemistr and Biophysics, Karolinska Institutet, Campus Solna, 17165 Stockholm, Sweden (1)
Emory University School of Medicine Departments of Biochemistry, Neurology (1)
Institut Pasteur (1)
Institute for Biology and Environmental Science, Dep. Evolutionary Genetics of Plants, Carl von Ossietzky Universität Oldenburg (1)
Institute for Genetics, UzK, Cologne, Germany (1)
Max-Planck Institute for Multidisciplinary Sciences Bionalaytical Mass Spectrometry Group University Medical Center Goettingen Bioanalytics Institute for Clincal Chemistry (1)
North Carolina State University, NC, USA (1)
Professor, Virology Director of the Laboratory of Molecular Virology, Discovery Hall, Manassas,VA 20110, USA (1)
Senior Group Leader, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland (1)
Structural Biology (1)
University of Halle-Wittenberg Institute for Biology – General Genetics Weinbergweg 10 06120 Halle (Saale) Germany (1)

IsPrivate

False (3)

Submitter Keywords

Immuno-oncology (2)

Classification

viruses (5)
bacteria (5)
fungi (1)
protozoa (1)

Study type

Transcription profiling by array (112)
RNA-seq of coding RNA (78)
ChIP-seq (55)
Other (25)
RNA-seq of non coding RNA (7)
CLIP-seq (6)
ChIP-chip by tiling array (5)
Unknown experiment type (4)
ChIP-chip by array (4)
Comparative genomic hybridization by array (4)
DNA-seq (4)
RIP-seq (3)
Methylation profiling by array (3)
Transcription profiling by SAGE (2)
Transcription profiling by tiling array (2)
RNAi profiling by array (2)
Genotyping by array (2)
Transcription profiling by RT-PCR (2)
ATAC-seq (2)
One-color microarray (1)
CLIP-Seq (1)
Cell line - One-color microarray (1)
Animal - High-throughput sequencing (1)
Cell line - High-throughput sequencing (1)
MicroRNA profiling by high throughput sequencing (1)
Proteomic profiling by array (1)
Methylation profiling by high throughput sequencing (1)
RNA-seq of total RNA (1)

Release Date

2013 (87)
2014 (80)
2015 (72)
2016 (67)
2025 (58)
2011 (57)
2022 (55)
2021 (55)
2023 (52)
2019 (50)
2012 (50)
2010 (45)
2018 (42)
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2017 (40)
2020 (30)
2009 (27)
2008 (24)
2005 (18)
2006 (15)
2007 (12)
2026 (10)
2004 (9)
2003 (8)
1998 (7)
1999 (5)
2002 (3)
2001 (3)
2000 (1)
1997 (1)

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Promoter directionality is controlled by U1 snRNP and polyadenylation signals

Transcription of the mammalian genome is pervasive, but productive transcription outside of protein-coding genes is limited by unknown mechanisms. In particular, although RNA polymerase II (RNAPII) initiates divergently from most active gene promoters, productive elongation occurs primarily in the s...

ORGANISM(S): Mus musculus

2013-06-28 | E-GEOD-46433 | biostudies-arrayexpress

iCLIP and NGS to map protein-RNA interactions for U1-snRNP proteins in Trypanosoma brucei

Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) combined with high-throughput sequencing was performed to generate genome-wide binding maps of two U1-snRNP proteins: U1C and U1-70K in Trypanosoma brucei. 3 (2) biological replicates of U1C (U1-70K) -specific co-immuno...

ORGANISM(S): Trypanosoma brucei

2014-05-16 | E-GEOD-43848 | biostudies-arrayexpress

Sequence specific recognition of U1 snRNP stem-loop 4 by the ubiquitin-like domain of U2 snRNP protein SF3A1 and its RGG motif

Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the interaction between the ubiquitin-like domain (UBL) of the protein SF3A1, a component of the U2 snRNP, with stem-loop 4 RNA (SL4) from the U1 snRNP. The complex was cross-linked and analysed both in ...

ORGANISM(S): Homo sapiens (Human)

2022-02-22 | PXD027189 | Pride