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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
TranscriptomicsPervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae
Protein-RNA interactions are integral components of nearly every aspect of biology including regulation of gene expression, assembly of cellular architectures, and pathogenesis of human diseases. However, studies in the past few decades have only uncovered a small fraction of the vast landscape of t...
ORGANISM(S): Saccharomyces cerevisiae 
2013-01-29 | E-GEOD-43747 | biostudies-arrayexpress
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