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MetabolomicsA multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6 (NMR assay)

Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that capt...

2020-02-14 | MTBLS1320 | MetaboLights
ProteomicsHybrid structural modeling of protein-RNA complexes using crosslinking of segmentally isotope labeled RNA and tandem mass spectrometry
To study protein-RNA interactions at single amino acid and single nucleotide resolution we developed a new approach, termed cross-linking of segmentally isotope labeled RNA and tandem mass spectrometry (CLIR-MS/MS). The method was developed using the PTBP1-EMCV IRES complex as a model system and add...
ORGANISM(S): Homo sapiens (Human) 
2017-03-27 | PXD005566 | Pride
Photochemical cross-linking  protein-rna cross-linking  segmental isotope labeling of rna  clir-ms/ms  ribonucleoproteins  structural proteomics  polypyrimidine tract binding protein 1  u1 snrnp 
TranscriptomicsThe mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [RNA-seq]
Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation and translation. We developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteom...
ORGANISM(S): Homo sapiens 
2012-06-01 | E-GEOD-38356 | biostudies-arrayexpress
UnknownA Genetically Encoded Diazirine Analogue for RNA-Protein Photo-crosslinking.
Not available
S-EPMC7003851 | biostudies-literature
TranscriptomicsTranscriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
This SuperSeries is composed of the following subset Series: GSE21574: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: QKI data GSE21575: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: IGF2BP data GSE215...
ORGANISM(S): Homo sapiens 
2010-04-29 | E-GEOD-21578 | biostudies-arrayexpress
ProteomicsDefining the RNA Interactome by Total RNA-Associated Protein Purification
UV crosslinking can be used to identify precise RNA targets for individual proteins, transcriptome-wide. We sought to develop a technique to generate reciprocal data, identifying precise sites of RNA-binding proteome-wide. The resulting technique, total RNA-associated protein purification (TRAPP), r...
ORGANISM(S): Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2019-03-26 | PXD011071 | Pride
Trapp rna-protein uv 
TranscriptomicsCold induced RNA-binding proteins influence alternative polyadenylation
We employed PAR-CLIP, a recently developed method based on RNA-protein crosslinking, to identify Cirbp and Rbm3 binding sites at transcriptome-level. Genome-wide RNA-seq analysis indicated that cold temperature leads to extensive 3M-bM-^@M-^YUTR lengthening whereas the loss of Cirbp or Rbm3 result...
ORGANISM(S): Mus musculus 
2013-05-01 | E-GEOD-40468 | biostudies-arrayexpress
UnknownStructure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes.
Not available
S-EPMC10937933 | biostudies-literature
GenomicsLive-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking
Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking
PRJNA417050 | ENA
TranscriptomicsMixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data
The Photo-Activatable Ribonucleoside-enhanced CrossLinking and ImmunoPrecipitation (PAR-CLIP) method was recently developed for global identification of RNAs interacting with proteins. The strength of this versatile method results from induction of specific T to C transitions at sites of interaction...
ORGANISM(S): Homo sapiens 
2012-08-07 | E-GEOD-37524 | biostudies-arrayexpress
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