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TranscriptomicsRNAcompete: a method for rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
Metazoan genomes encode hundreds of RNA binding proteins (RBPs) but relatively few have well-defined RNA-binding preferences. Current techniques for determining RNA targets, including those involving in vitro selection and RNA co-immunoprecipitation, require significant time and labour investment. H...
ORGANISM(S): synthetic construct 
2010-05-18 | E-GEOD-15769 | biostudies-arrayexpress
TranscriptomicsRNA-Binding Protein targets in Saccharomyces cerevisiae
The vast landscape of RNA-protein interactions at the heart of post-transcriptional regulation remains largely unexplored. Indeed it is likely that, even in yeast, a substantial fraction of the regulatory RNA-binding proteins (RBPs) remain to be discovered. Systematic experimental methods can play a...
ORGANISM(S): Saccharomyces cerevisiae 
2011-03-10 | E-GEOD-22876 | biostudies-arrayexpress
OtherInsights into RNA biology from an atlas of mammalian mRNA-binding proteins.
Data from ProteomeXchange, PXD ID: PXD002880. Experiment: KS_A4_3, file: folder summary. Published as part of Cell. 2012 Jun 8;149(6):1393-406 . From the Abstract: {{i}} RNA-binding proteins (RBPs) determine RNA fate from synthesis to decay. Employing two complementary protocols for covalent UV cro...
ORGANISM(S): Homo_sapiens_viruses, Human_female 
GPM11210041750 | GPMDB
Resource Reanalysis 
ProteomicsDynamic interactions of RNA binding proteins to human cytokine mRNA govern T cell responses
Effective T cell responses against infections and tumors depend on the production of effector molecules, including the key pro-inflammatory cytokines IFN-γ, TNF-α and IL-2. Recent studies revealed that post-transcriptional events determine the magnitude and duration of cytokine production in T cells...
ORGANISM(S): Homo sapiens (Human) 
2023-04-20 | PXD028171 | Pride
Rna-binding proteins 
TranscriptomicsA quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins (CLIP)
Crosslinking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins (RBPs). We developed a method for CLIP data analysis and applied it to compare 254 nm CLIP with PAR-CLIP, which involves crosslinking of photoreactive nucleotides with 365...
ORGANISM(S): Homo sapiens 
2011-05-15 | E-GEOD-28859 | biostudies-arrayexpress
TranscriptomicsA quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins (mRNA-seq)
Crosslinking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins (RBPs). We developed a method for CLIP data analysis and applied it to compare 254 nm CLIP with PAR-CLIP, which involves crosslinking of photoreactive nucleotides with 365...
ORGANISM(S): Homo sapiens 
2011-05-15 | E-GEOD-28864 | biostudies-arrayexpress
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
ProteomicsLarge-scale identification of RNA-binding proteins
We developed a method, which enables unbiased, systematic identification of RBPs. Applying this method, we identified a large number of RBPs, adding hundreds of candidate RBPs to those previously known. In addition, we plotted the first large-scale distribution profile of RBPs after inhibition of RN...
ORGANISM(S): Homo sapiens (Human) 
2021-09-09 | PXD023162 | Pride
Rna-binding proteins(rbps)  lc-msms  large-scale 
TranscriptomicsEffects of deletion of genes encoding RNA-binding proteins on gene expression in S. pombe
To study the contribution of RNA-binding proteins (RBPs) to the regulation of RNA turnover, we used DNA microarrays to examine the transcriptome of S. pombe strains containing deletions in non-essential genes encoding RBPs
ORGANISM(S): Schizosaccharomyces pombe 
2014-11-06 | E-MTAB-2314 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: IGF2BP data
To test the influence of IGF2BPs on the stability of their interacting mRNAs, as reported previously for some targets (Yisraeli, 2005), we simultaneously depleted all three IGF2BP family members using siRNAs and compared the cellular RNA from knockdown and mock-transfected cells on microarrays. The ...
ORGANISM(S): Homo sapiens 
2010-05-27 | E-GEOD-21575 | biostudies-arrayexpress
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