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TranscriptomicsWidespread Occurrence of m6A in bacterial mRNA
N6-methyladenosine (m6A) is one of the most abundant modifications in eukaryotic RNA. Recent mapping of m6A methylomes in mammals, yeast, and plants as well as characterization of m6A methyltransferases, demethylases, and binding proteins have revealed regulatory functions of this dynamic RNA modifi...
ORGANISM(S): Pseudomonas aeruginosa PAO1 
2015-07-08 | E-GEOD-65347 | biostudies-arrayexpress
TranscriptomicsIdentification of RNAs associated with the Caenorhabditis elegans spliced-leader trans-splicing proteins SNA-2, SNA-3, SNR-2 and SUT-1 proteins by RIP-Seq.
This study aimed to identify RNAs bound to the C. elegans SNA-2, SNA-3, SUT-1 and SNR-2 proteins involved in spliced leader 1 trans-splicing through use of RNA immunoprecipitation sequencing (RIP-Seq). Four IP sample replicates and four control sample replicates were sequenced for each protein.
ORGANISM(S): Caenorhabditis elegans 
2024-04-24 | E-MTAB-13193 | biostudies-arrayexpress
TranscriptomicsGenome-wide identification of transcripts associated with lncRNA-ATB by RIP-seq
The role of TGF-β-induced epithelial-mesenchymal transition (EMT) in cancer cell dissemination is well established, but the involvement of lncRNAs in TGF-β signaling is still unknown. In this study, we observed that the lncRNA-Activated by TGF-β (lncRNA-ATB) was upregulated in hepatocellular carcino...
ORGANISM(S): Homo sapiens 
2014-02-08 | E-GEOD-54799 | biostudies-arrayexpress
TranscriptomicsAnalysis of the role of yeast Sro9p in controlling the translation of specific mRNAs
The mechanisms by which RNA-binding proteins control the translation of subsets of mRNAs are not yet clear. Sro9p is an atypical La motif containing protein (LARP). LARPs are members of a superfamily of RNA-binding proteins conserved across eukaryotes. We performed transcriptomics and RIP-Seq analys...
ORGANISM(S): Saccharomyces cerevisiae 
2015-05-01 | E-MTAB-2568 | biostudies-arrayexpress
TranscriptomicsAnalysis of the role of yeast Slf1p in translation of specific mRNAs during oxidative stress response
The mechanisms by which RNA-binding proteins control the translation of subsets of mRNAs are not yet clear. Slf1p is an atypical La motif containing protein (LARP). LARPs are members of a superfamily of RNA-binding proteins conserved across eukaryotes. We performed transcriptomics and RIP-Seq analys...
ORGANISM(S): Saccharomyces cerevisiae 
2015-05-01 | E-MTAB-2567 | biostudies-arrayexpress
ProteomicsProtein Interactome of U2AF2 during T cell activation
T cell activation leads to dramatic changes in cellular phenotype. We used activated human CD4 T cells to study how RNA binding proteins define the post-transcriptional landscape. Using RIPseq, we identified the RNA interactome of U2AF2 and show that U2AF2 binds the majority of transcripts that are...
ORGANISM(S): Homo sapiens (Human) 
2016-04-27 | PXD001843 | Pride
Rip mass spectrometry U2af Cd4 t cells Rna-binding proteins 
ProteomicsIdentifying lncRNA-protein interactions in hematopoietic progenitor cells by hybridization capture and mass spectrometry
Long non-coding RNAs (lncRNAs) exert regulatory functions in a wide spectrum of biological contexts, and certain regulatory functions involve the formation of RNA-protein complexes. Discovering the structure/function of these complexes may unveil important functional insights. The DDX41 gene encodin...
ORGANISM(S): Mus musculus (Mouse) 
2025-07-17 | PXD062695 | Pride
Lncrna  lncrna-protein interaction  hematopoiesis  mass spectrometry  proteomics  hybridization capturelncrna  lncrna-protein interaction  hematopoiesis  mass spectrometry  proteomics  hybridization capture 
UnknownThe Coxsackievirus and Adenovirus Receptor (CAR) undergoes ectodomain shedding and regulated intramembrane proteolysis (RIP).
Not available
S-EPMC3756012 | biostudies-literature
ProteomicsSILAC Mass Spectrometry of U2AF2 Interactome in Resting and Activated CD4 T cells
T cell activation leads to dramatic changes in cellular phenotype. We used activated human CD4 T cells to study how RNA binding proteins define the post-transcriptional landscape. Using RIPseq, we identified the RNA interactome of U2AF2 and show that U2AF2 binds the majority of transcripts that are...
ORGANISM(S): Homo sapiens (Human) 
2016-04-27 | PXD001846 | Pride
Cd4 t cell activation/mrna splicing/rna-binding proteins/u2af 
ProteomicsClamping down on transcription: repression of archaeal RNAP by the novel viral regulator RIP
Little is known about how archaeal viruses perturbate the transcription machinery of their hosts. We provide the first example of a non-DNA binding archaeo-viral transcription factor that directly targets the host RNA polymerase and efficiently represses its activity. We have used cross-linking and ...
ORGANISM(S): Sulfolobus solfataricus 
2016-12-02 | PXD003282 | Pride
Transcription Evolution Virus Repressor Cross-linking and mass spectrometry Rna polymerase Archaea Bacteriophages 
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