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ProteomicsIdentification of proteins and miRNAs that specifically bind an mRNA in vivo
Understanding regulation of an mRNA requires knowledge of its regulators. However, methods for reliable de-novo identification of proteins binding to a particular RNA are scarce and were so far only successfully applied to abundant noncoding RNAs in cell culture. Here, we present vIPR, an RNA-protei...
ORGANISM(S): Caenorhabditis elegans 
2019-08-12 | PXD013720 | Pride
Q exactive hf-x Caenorhabditis elegans Rna pulldown Q exactive plus 
UnknownIdentification of proteins and miRNAs that specifically bind an mRNA in vivo.
Not available
S-EPMC6746756 | biostudies-literature
TranscriptomicsIn vivo and transcriptome-wide identification of RNA-binding protein target sites [PAR-CLIP]
Animal mRNAs are regulated by hundreds of RNA binding proteins (RBPs). The identification of RBP targets is crucial for understanding their function. A recent method, PAR-CLIP, uses photoreactive nucleosides to crosslink RBPs to target RNAs in cells prior to immunoprecipitation. Here, we establish i...
ORGANISM(S): Caenorhabditis elegans 
2011-12-09 | E-GEOD-33569 | biostudies-arrayexpress
TranscriptomicsA variety of Dicer substrates in human and C. elegans (HEK small RNA)
The endoribonuclease Dicer is known for its central role in the biogenesis of eukaryotic small RNAs/microRNAs. Despite its importance, Dicer target transcripts have not been directly mapped. Here, we apply biochemical methods to human cells and C. elegans and identify thousands of Dicer binding site...
ORGANISM(S): Homo sapiens 
2014-11-20 | E-GEOD-63458 | biostudies-arrayexpress
ProteomicsB-cell-specific MYD88 L252P expression causes a premalignant gammopathy resembling IgM MGUS
A highly recurrent, somatic L265P mutation in the TIR domain of the signaling adapter MYD88 constitutively activates NF-kB. It occurs in nearly all human patients with Waldenström’s macroglobulinemia (WM), a B cell malignancy caused by IgM-expressing cells. Here we introduced an inducible leucine to...
ORGANISM(S): Mus musculus (Mouse) 
2020-11-06 | PXD017292 | Pride
Lymphoid neoplasia 
TranscriptomicsTranscriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (small RNA AGO-IP)
Dicer is a deeply conserved endoribonuclease with key functions in small RNA biogenesis. Here we employed PAR-CLIP/iPAR-CLIP to identify direct Dicer binding sites in the transcriptomes of human cells and human. We found hundreds of novel miRNAs and non-canonical Dicer substrates with high sensitivi...
ORGANISM(S): Homo sapiens 
2014-11-20 | E-GEOD-55331 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of miRNA expression among various mouse hematopoietic cell types and hippocampal tissue
Compare miRNA expression among various hematopoietic cell types and hippocampal tissue
ORGANISM(S): Mus musculus 
2005-12-01 | E-MEXP-372 | biostudies-arrayexpress
GenomicsChIP-Seq of human endogenous small RNAs associated to Argonaute 1 and 2
Small non-coding RNAs function in concert with Argonaute (Ago) proteins to regulate gene expression at the level of transcription, mRNA stability or translation. Ago proteins bind small RNAs and form the core of silencing complexes. Here we report the analysis of small RNAs associated with human ...
ORGANISM(S): Homo sapiens 
2008-11-20 | E-GEOD-13370 | biostudies-arrayexpress
TranscriptomicsConserved functional antagonism between CELF and MBNL proteins regulates stem cell-specific alternative splicing and regeneration in planarians
Understanding gene regulation in stem cells is key to understanding stem cell biology. Contrary to transcriptional regulation the function of alternative splicing (AS) in stem cells is poorly understood. Here we study function and mechanisms of AS in a powerful in vivo model for stem cell biology, t...
ORGANISM(S): Schmidtea mediterranea 
2016-08-01 | E-GEOD-75594 | biostudies-arrayexpress
TranscriptomicsThe Notch/Hes1 pathway sustains NF-M-NM-:B activation through CYLD repression in T cell leukemia
The NF-M-NM-:B pathway is a critical regulator of the immune system and has been implicated in cellular transformation and tumorigenesis. NF-M-NM-:B response is regulated by the activation state of the IM-NM-:B kinase (IKK) complex and triggered by a wide spectrum of stimuli. We previously reported ...
ORGANISM(S): Homo sapiens 
2011-05-07 | E-GEOD-20667 | biostudies-arrayexpress
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