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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
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
TranscriptomicsExtensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
This SuperSeries is composed of the following subset Series: GSE3968: Puf proteins, RNA co-immunopurification GSE3969: Puf3delta vs. wild type comparison Abstract: Genes encoding RNA-binding proteins are diverse and abundant in eukaryotic genomes. Although some have been shown to have roles in post...
ORGANISM(S): Saccharomyces cerevisiae 
2006-03-07 | E-GEOD-4393 | 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 
TranscriptomicsProteomic profiling by array of yeast E2Bmin, mRNA and total RNA on fuctional protein microarrays to identify RNA-binding proteins
Application of different sorts of RNAs (E2Bmin, mRNA, total RNA) on functional protein micorarrays to identify RNA-binding proteins.
ORGANISM(S): Saccharomyces cerevisiae 
2011-09-01 | E-MEXP-2897 | biostudies-arrayexpress
TranscriptomicsEffects of deletion of RNA-binding proteins on RNA stability
To investigate the contribution of RNA-binding proteins to the regulation of RNA decay we used an in vivo labelling system (Cleary et al. 2005 Nat Biotechnol. 23, 232-7) to estimate the decay rates of RBP mutants and wild type S. pombe cells
ORGANISM(S): Schizosaccharomyces pombe 
2014-11-06 | E-MTAB-2712 | biostudies-arrayexpress
TranscriptomicsRIp-chip experiments with the Scw1, Zfs1 and Red1 RNA-binding proteins
We have used RIp-chip to identify mRNAs that coprecipitae with specific RNA-binding proteins
ORGANISM(S): Schizosaccharomyces pombe 
2014-11-06 | E-MTAB-2709 | biostudies-arrayexpress
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 
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
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