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ProteomicsAnalysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry
Protein–DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein–DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of protei...
ORGANISM(S): Homo sapiens (Human) Xenopus laevis (African clawed frog) 
2020-10-20 | PXD020290 | Pride
Mass spectrometry Protein-dna interactions Uv-cross-linking 
ProteomicsStructural insights into protein-RNA interactions within biomolecular condensates using UV cross-linking and mass spectrometry
UV-light-induced protein-RNA cross-linking followed by MS analysis was used to identify the interaction sites between protein and RNA in different phase-separated and non-phase separated states of complexes involving the following proteins: PTBP1, FUS, and SARS-CoV-2 nucleocapsid protein.
ORGANISM(S): Homo sapiens (Human) Severe acute respiratory syndrome coronavirus 2 
2024-03-06 | PXD046267 | Pride
Protein-rna cross-linking Uv cross-linking Protein-rna complexes Biomolecular condensates Liquid-liquid phase separation 
GenomicsUV cross-linking RIP-seq of VSV-GFP-infected HEK293T cells overexpressed PTENα
UV cross-linking RIP-seq of VSV-GFP-infected HEK293T cells overexpressed PTENα
PRJNA903837 | ENA
ProteomicsStructural requirements for photo-induced RNA-protein cross-linking
Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the UV cross-linking behavior of in vitro reconstituted FOX1 RRM in complex with its cognate RNA sequence, the Fox binding element (FBE), (U)GCAUGU. The FBE heptanucleotide was subsequently mutated, and ...
ORGANISM(S): Homo sapiens (Human) 
2022-06-09 | PXD031381 | Pride
Uv cross-linking  mbnl1  fox1  ptbp1  sf3a1  u1  u2  cross-linking  xl-ms  structural proteomics  protein-rna  rna-protein  protein-rna complex  rna-protein complex  clir-ms 
TranscriptomicsUV cross-linking RIP-seq of VSV-GFP-infected HEK293T cells overexpressed PTENα
To determine whether PTENα directly binds to viral RNA or host mRNA, we performed UV cross-linking RNA immunoprecipitation (RIP) sequencing of HEK293T cells transfected with vector encoding PTENα under VSV-GFP (green fluorescent protein-expressing vesicular stomatitis virus) infection
ORGANISM(S): Homo sapiens 
2024-02-19 | GSE218439 | GEO
ProteomicsSensitive detection and structural characterisation of UV-induced cross-links in protein-ribonucleic acid complexes using stable isotope labelling and mass spectrometry
The recently introduced cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) technique enables protein-RNA cross-links to be used as precisely localized distance restraints in de novo structural modelling, but little is known about the structural characteristics of UV-induc...
ORGANISM(S): Homo sapiens (Human) 
2023-09-06 | PXD029930 | Pride
Uv cross-linking  mbnl1  fox1  ptbp1  sf3a1  u1  u2  cross-linking  xl-ms  structural proteomics  protein-rna  rna-protein  protein-rna complex  rna-protein complex  clir-ms 
GenomicsTotal RNA-seq of L. mexicana promastigotes and axenic amastigotes following UV-cross-linking and orthogonal organic phase separation
Total RNA-seq of L. mexicana promastigotes and axenic amastigotes following UV-cross-linking and orthogonal organic phase separation
PRJNA778524 | ENA
UnknownMutation enrichment in human DNA samples via UV-mediated cross-linking.
Not available
S-EPMC8989544 | biostudies-literature
ProteomicsSingle Nucleotide Resolution RNA-Protein Cross-Linking/MS: Simple Extension of the CLIR-MS Workflow
RNA-protein interactions mediate a vast number of intracellular processes. CLIR-MS (cross-linking of isotope labeled RNA and tandem mass spectrometry) is a mass spectrometric technique that allows the identification of RNA-protein interaction sites at single nucleotide/amino acid resolution in a sin...
ORGANISM(S): Homo sapiens (Human) 
2021-11-04 | PXD024010 | Pride
Protein rna cross-linking clir-ms uv xl 
UnknownEnhanced UV Penetration and Cross-Linking of Isoporous Block Copolymer and Commercial Ultrafiltration Membranes using Isorefractive Solvent.
Not available
S-EPMC11434031 | biostudies-literature
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