Long loop - OmicsDI

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Organisms

Homo sapiens (156)
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biostudies-arrayexpress (927)
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Technology Type

Mass Spectrometry (189)
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MSE (3)
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NMR spectroscopy assay (1)
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Instrument Platform

Illumina HiSeq 2000 (20)
Illumina NovaSeq 6000 (18)
Illumina HiSeq 2500 (15)
NextSeq 500 (14)
Illumina HiSeq 4000 (11)
ScanArray Express HT (6)
HiSeq X Ten (4)
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Flat panel airlift-loop reactor with a 1.7 L working volume (2)
Maxwell® 16 LEV simplyRNA Tissue kit (Promega) (2)
Anaerobic workstation with airlock (2)
GenePix 4000A [Axon Instruments] (2)
Axon GenePix 4000B scanning hardware (2)
Illumina HiSeq 1500 (2)
NextSeq 550 (2)
Chromium Next GEM Chip G (1)
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. (1)
Illumina iScan microarray scanner (1)
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Chromium Single Cell 5' Library & Gel Bead Kit v2 (1)
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Qubit 3.0 and Nanodrop Lite (1)
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Illumina Human-12 v1 Expreesion BeadChip (1)
BD FACS JAZZ (1)

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2008 (64)
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2018 (44)
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2019 (30)
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2006 (9)
2004 (7)

UNIPROT ID/AC

P61225 (4)
P51452 (4)
P27361 (4)
P04049 (4)
Q02750 (4)
P04637 (4)
Q00987 (4)
Q13315 (2)
O95257 (1)
P24522 (1)
O75293 (1)
P38936 (1)
P09560 (1)
Q16539 (1)
Q8N726 (1)
Q05116 (1)
P26696 (1)

ENSEMBL ID

ENSG00000141510 (2)
ENSG00000135679 (2)
ENSG00000147889 (1)

CHEBI ID

CHEBI:7916 (6)
CHEBI:16704 (6)
CHEBI:30769 (6)
CHEBI:18012 (5)
CHEBI:30887 (5)
CHEBI:16027 (5)
CHEBI:27897 (5)
CHEBI:28527 (4)
CHEBI:16335 (4)
CHEBI:17509 (4)
CHEBI:16467 (4)
CHEBI:30797 (4)
CHEBI:16919 (4)
CHEBI:15756 (4)
CHEBI:16991 (3)
CHEBI:169821 (3)
CHEBI:140765 (3)
CHEBI:169640 (3)
CHEBI:271436 (3)
CHEBI:17890 (3)
CHEBI:31130 (3)
CHEBI:18471 (3)
CHEBI:75633 (3)
CHEBI:168762 (3)
CHEBI:142593 (3)
CHEBI:67206 (3)
CHEBI:28733 (3)
CHEBI:30778 (3)
CHEBI:33699 (2)
CHEBI:26523 (1)

Metabolite Name

Citric acid (3)
Cytosine (3)
Phenylalanine (3)
Linoleic acid (3)
Creatine (3)
Sophoraisoflavanone D (2)
PG(12:0/14:1(9Z)) (2)
(23E)-26,26,26,27,27,27-hexafluoro-1alpha,25-dihydroxy-23,24-didehydrovitamin D3 / (23E)-26,26,26,27,27,27-hexafluoro-1alpha,25-dihydroxy-23,24-didehydrocholecalciferol (2)
Okanin 4-methyl ether 4'-O-(2''-O-caffeoyl-6''-O-acetylglucoside) (2)
Butyl 3'-O-butanoyl-4,6,4'-tri-O-(2-methylpropanoyl)-neohesperidoside (2)
Cyclopassifloside VII (2)
Amorphigenin O-glucoside (2)
2-hydroxymethylolanzapine (2)
5,7-Dihydroxy-3',4'-dimethoxy-5'-prenylflavanone (2)
VD 2716 (2)
7,7-Difluoro-8Z-dodecenyl acetate (2)
2-O-(beta-D-galactopyranosyl-(1->6)-beta-D-galactopyranosyl) 2S-hydroxyundecanoic acid (2)
Stoloniferone E (2)
Bismahanine (2)
Avenanthramide C (2)
Cis-p-Coumaroylcorosolic acid (2)
Linalool 3,6-oxide primeveroside (2)
3-Methoxy-4,5-methylenedioxycinnamaldehyde (2)
3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid (2)
N-Carbamoyl glucuronide lorcaserin (2)
Glisoxepide (2)
Palmidin C (2)
Norrubrofusarin 6-beta-gentiobioside (2)
Butyl butyryllactate (2)
4'-N-desmethylolanzapine (2)

First Public Date

2025 (76)
2024 (60)
2023 (54)
2026 (52)
2022 (47)
2020 (38)
2014 (33)
2021 (30)
2018 (25)
2019 (21)
2017 (11)
2016 (10)
2013 (9)
2015 (8)

Modelling Approach

Ordinary differential equation model (51)

Lab affiliation

Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic (41)
Department of Chemistry, National and Kapodistrian University of Athens, 15784 Zografou, Greece (5)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (4)
Virginia Tech (4)
School of Medicine, National Kapodistrian University of Athens, Mikras Asias 75, Athens 115 27, Greece (3)
Virginia Tech, Biological Sciences (3)
1Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens, 15784, Greece. 2Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, 70013, Greece. (2)
Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, China. (2)
Chair of Proteomics and Bioanalytics, Technical University of Munich, Germany (2)
Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece (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)
Department of Chemistry & Chemical Biology, Northeastern University (2)
Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (2)
Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas (FORTH), 100, Plastira Str., 70013 Heraklion, Crete, Greece. (2)
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (2)
Program in Molecular Medicine, UMass Chan Medical School (2)
Queensland Brain Institute, The University of Queensland, St Lucia Campus (Brisbane), QLD 4072, Australia (2)
School of Pharmacy, Sungkyunkwan University, South Korea (2)
1-University of Lille, CNRS, UAR 3290, MSAP, Miniaturisation pour la Synthèse l'Analyse et la Protéomique, F-59650 Villeneuve d’Ascq, France 2-Shrieking sixties, 1-3 Allée Lavoisier, F-59650 Villeneuve d'Ascq, France. (1)
1Human Embryonic and Induced Pluripotent Stem Cell Unit, Hellenic Pasteur Institute, Athens, Greece 2Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Hellenic Pasteur Institute, Athens, Greece (1)
Analytical Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy (1)
Benaki Phytopathological Institute, 8 Stefanou Delta Str., 14561 Athens, Greece. (1)
Biomedical Research Institute, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece (1)
Biomedical Research in Melanoma-Animal Models and Cancer Laboratory Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Hospital Barcelona-UAB Barcelona, 08035, Spain. (1)
Biomolecular Mass Spectrometry and Proteomics groups, Utrecht University (1)
Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110 Ioannina, Greece (1)
Biotechnology Laboratory, Department of Biological Applications and Technologies, Universityof Ioannina, 45110 Ioannina, Greece (1)
Brown University (1)
CEITEC-MU, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic (1)
CEITEC—Central European Institute of Technology, Masaryk University, Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic (1)

IsPrivate

False (51)

Model Flag

Non Miriam (1)

Classification

viruses (3)
protozoa (3)
bacteria (2)

Modification

2x(15)N labeled L-lysine (2)
4x(15)N labeled L-arginine (2)

Study type

Transcription profiling by array (583)
RNA-seq of coding RNA (110)
ChIP-seq (45)
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Unknown experiment type (25)
Other (22)
Transcription profiling by RT-PCR (14)
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Animal - High-throughput sequencing (3)
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2000 (12)
2003 (10)
2001 (10)
1999 (6)
1998 (4)
1997 (2)

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Nucleolin uses its RBD2 domain to recognize long-loop G-Quadruplexes from human minisatellite CEB25

We investigated herein the interaction between nucleolin (NCL) and a set of G4 sequences derived from the CEB25 human minisatellite which adopt a parallel topology while differing by the length of the central loop (from 9nt to1nt). It is revealed that NCL strongly binds to long-loop (9-5 nt) G4 whil...

ORGANISM(S): Homo sapiens (Human)

2020-03-19 | PXD016529 | Pride

CRISPR-assisted RNA-protein interaction detection (CARPID) combined with quantitative mass spectrometry was used to identify proteins interacting with the long non-coding RNA (lncRNA) Taurine Up-regulated 1 (TUG1) in HEK293T cells under physiological conditions and after Camptothecin (CPT) treatment.

This project utilized CRISPR-assisted RNA-protein interaction detection (CARPID) combined with mass spectrometry to identify proteins interacting with the long non-coding RNA (lncRNA) TUG1 in HEK293T cells. TUG1 preferentially interacts with known R-loop-associated proteins, particularly under Campt...

ORGANISM(S): Homo Sapiens (human)

2025-07-17 | PXD049137 | JPOST Repository

CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire

PRJNA1305318 | ENA

LoopSeq Synthetic Long Read Sequencing Uncovers Isoform Modulation in the progression of Colon Cancer [Loop QC]

PRJNA656369 | ENA

SRF promotes long-range chromatin loop formation and stem cell pluripotency

PRJNA1076243 | ENA

A long noncoding RNA regulates sister chromatid cohesion [ChIP-seq]

Long noncoding RNAs (lncRNAs) have appeared to be involved in the most diverse cellular processes through multiple mechanisms. Here we describe a previously uncharacterized human lncRNA, CONCR (cohesion regulator noncoding RNA), transcriptionally activated by MYC, which is upregulated in multiple ca...

ORGANISM(S): Homo sapiens

2016-08-03 | E-GEOD-81600 | biostudies-arrayexpress

High-Throughput Single-Molecule R-loop Footprinting Reveals Principles of R-loop Formation

PRJNA541182 | ENA

A long noncoding RNA regulates sister chromatid cohesion [RNA-seq]

ORGANISM(S): Homo sapiens

2016-08-03 | E-GEOD-81601 | biostudies-arrayexpress

A long noncoding RNA regulates sister chromatid cohesion [microarray]

ORGANISM(S): Homo sapiens

2016-08-03 | E-GEOD-81599 | biostudies-arrayexpress

CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire [3C-HTGTS]

PRJNA1215321 | ENA

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