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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 
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 
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 
ProteomicsGlobal RNA-Protein Interactome purification screening identifies RRP1 in IL-1-stimulated BMDM cells
An “unbiased” approach that holds promise for isolating total protein-RNA complexes from whole cell samples without any labeling and identifying RBPs that lack classical RNA-binding domains (RBDs) or that bind different RNA classes is greatly needed. On the other hand, due to the scarcity of primary...
ORGANISM(S): Mus musculus (Mouse) 
2025-07-04 | PXD054800 | Pride
Rna-binding protein  primary macrophages  il-1 
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 
TranscriptomicsTranscriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: sequencing data
We applied 4-thiouridine to cultured cells expressing the FLAG/HA-tagged RNA-binding proteins (RBPs) followed by UV 365 nm irradiation. The crosslinked RNA-protein complexes were isolated by immunoprecipitation, and the covalently bound RNA was partially digested with RNase T1 and radiolabeled. The ...
ORGANISM(S): Homo sapiens 
2010-05-21 | E-GEOD-21918 | biostudies-arrayexpress
ProteomicsNon-poly(A) RNA Interactome capture (RIC) of mouse liver
Male mice on a homogenous C57BL6/J genetic background were sacrificed at 11 to 13 weeks of age by cervical dislocation. Liver were immediately harvested, flash frozen in liquid nitrogen and stored at -80°C until use. Animal handling was in accordance with guidelines approved by the European Molecula...
ORGANISM(S): Mus musculus (Mouse) 
2023-03-02 | PXD038099 | Pride
Rna interactome capture. Rbp Ric Eric Rna binding protein Rbpome 
UnknownThe kinesin motor KIF1C is a putative transporter of the exon junction complex in neuronal cells.
Not available
S-EPMC9808568 | biostudies-literature
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 
ProteomicsRemodeling of RNA-Binding Proteome and RNA-mediated regulation as a new layer of control of sporulation
Sporulation allows certain bacteria to survive extreme conditions for extended periods posing challenges to public health and food safety. Transcriptional level of regulation relying on σ factors has been well studied in the non-pathogenic model Bacillus subtilis, while post-transcriptional control...
ORGANISM(S): Bacillus subtilis subsp. subtilis str. 168 Bacteria 
2025-08-13 | PXD061929 | Pride
Rna binding proteome Orthogonal organic phase separation Ooops Rbpome Bacillus subtilis Sporulation 
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