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ProteomicsThe Human RNA-Binding Proteome and Its Dynamics during Translational Arrest
The data presented here was produced using XRNAX - a novel extraction method for protein-crosslinked RNA from UV-crosslinked cells. We apply XRNAX for three proteomic downstream applications. First, we purify ribonucleotide-crosslinked peptides from XRNAX extracts and use their identification as dir...
ORGANISM(S): Homo sapiens (Human) 
2018-12-06 | PXD010520 | Pride
Uv-crosslinking Nucleotide-crosslinked peptides Xrnax Protein-crosslinked rna extraction Rna-binding proteins Arsenite stress Translational arrest Human rna-binding proteome Ribophagy 
ProteomicsCAPRI RNA binding proteins and domains in Drosophila and Humans
In the current work, we present a comprehensive coverage of the RNA-binding protein (RBP) interactome of Drosophila at four levels of resolution. The highest level tackled in our study represents the RNA-protein complexes, which we address by combining formaldehyde crosslinking of Drosophila S2 cell...
ORGANISM(S): Homo sapiens (Human) Drosophila melanogaster (Fruit fly) 
2019-07-02 | PXD013338 | Pride
Rna crosslinked peptides Rna protein interaction 
ProteomicsLPS-Stimulated Mouse Macrophage RNA Binding Protein Domain Enrichment and Analysis
Immortalized mouse macrophages (IMMs) were stimulated with lipopolysaccharide (LPS). RNA and RNA associated proteins were UV crosslinked, and sites of RNA-association were identified using LC-MS proteomics.
ORGANISM(S): Mus musculus (Mouse) 
2024-02-27 | PXD046793 | Pride
Macrophage Lps Mouse Rna binding protein 
ProteomicsUV-crosslinking mapping of LARP6 interaction sites with RNA
To map the regions of LARP6 that interacts directly with RNA, we developed a mass spectrometry-based approach termed IP-OOPS (Immunoprecipitation coupled with Orthogonal Organic Phase Separation. This approach combines the isolation of UV-C crosslinked RNA–protein adducts via Orthogonal Organic Phas...
ORGANISM(S): Homo sapiens (Human) 
2026-01-22 | PXD064029 | Pride
Lc-ms/ms  rna-protein interactions  organic phase separation  rna crosslinking 
ProteomicsRBS-ID: Comprehensive identification of RNA-binding sites at single amino acid-resolution
We developed RBS-ID, which greatly simplifies the RNA moiety by chemical cleavage, reducing the complexity of MS/MS search space to accurately identify and localize RBS in peptides. RBS-ID comprehensively and robustly identifies RNA-binding sites at both proteome and single protein level.
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2020-06-02 | PXD016254 | Pride
Human Rbp. rbs Rna Lc-ms/ms 
ProteomicsUnbiased characterization and systematic profiling of metabolically labeled RNA-binding sites
Here we introduce pRBS-ID, an amenable platform that enables robust profiling of PAR-crosslinked RBSs. Using tandem mass spectrometry (MS/MS) approaches, we unbiasedly characterize the PAR adducts on peptides, to develop an optimal MS/MS search pipeline that enables robust identification and quantif...
ORGANISM(S): Homo sapiens (Human) 
2021-11-02 | PXD023401 | Pride
Human Lc-ms/ms 
ProteomicsTargeted RNase H-mediated Extraction of crosslinked RBPs (TREX) for assessing U1 RNA interactome
We used Targeted RNase H-mediated Extraction of crosslinked RBPs (TREX)to assess the endogenous binding partners of U1 small nuclear RNA (U1 snRNA) in human HCT116 cells. Extracted proteins from U1 digested and control cells (5 replicate per condition) were compared, using label-free (LFQ) Quantitat...
ORGANISM(S): Homo sapiens (Human) 
2023-12-27 | PXD044643 | Pride
Trex  rbp  rna interactome  lc-ms/ms  quantitative proteomics 
ProteomicsChemoproteomic capture of RNA binding activity in living cells
Proteomic methods for RNA interactome capture (RIC) rely principally on crosslinking native or labeled cellular RNA to enrich and investigate RNA-binding protein (RBP) composition and function in cells. The ability to measure RBP activity at individual binding sites by RIC, however, has been more ch...
ORGANISM(S): Homo sapiens (Human) 
2023-10-10 | PXD044625 | Pride
Lc-msms Chemoproteomics Human Chemical biology Rna-binding protein Rna interactome 
ProteomicsTargeted RNase H-mediated Extraction of crosslinked RBPs (TREX) for assessing region-specific NORAD lncRNA interactome
We used Targeted RNase H-mediated Extraction of crosslinked RBPs (TREX)to assess the endogenous binding partners of the ND4 segment of NORAD long noncoding RNA (lncRNA) in human HCT116 cells. Extracted proteins from RNase H digested and control cells (4 replicate per region per condition) were compa...
ORGANISM(S): Homo sapiens (Human) 
2023-12-27 | PXD045385 | Pride
Norad  nd4  lncrna  trex  rbp  rna interactome  lc-ms/ms  quantitative proteomics 
ProteomicsRBDmap - Comprehensive Identification of RNA-Binding Domains in Human Cells
The RNA interactomes of HeLa and HEK293 cells jointly comprise 1106 RNA-binding proteins (RBPs), with almost half of these lacking well-defined RNA-binding domains (RBDs), suggesting the existence of numerous unknown RNA-binding architectures. Here, we report on “RBDmap”, a new method built on inter...
ORGANISM(S): Homo sapiens (Human) 
2016-08-08 | PXD000883 | Pride
Rna binding domain Rna-binding proteins 
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