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TranscriptomicsIntegrative AUF1 PAR-CLIP analysis uncovers AUF1 roles in translation and genome integrity (PAR-CLIP)
We report that AUF1 modulates global mRNA stability and translation, in turn promoting the maintenance of DNA integrity. Please see individual series. In short, for AUF1 PAR-CLIP, the four isoforms of AUF1 (p37, p40, p42, and p45) tagged with a Flag epitope were expressed in HEK293 cells. For total ...
ORGANISM(S): Homo sapiens 
2014-11-05 | E-GEOD-52971 | biostudies-arrayexpress
TranscriptomicsMixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data
The Photo-Activatable Ribonucleoside-enhanced CrossLinking and ImmunoPrecipitation (PAR-CLIP) method was recently developed for global identification of RNAs interacting with proteins. The strength of this versatile method results from induction of specific T to C transitions at sites of interaction...
ORGANISM(S): Homo sapiens 
2012-08-07 | E-GEOD-37524 | biostudies-arrayexpress
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
TranscriptomicsPAR-CLIP-seq reveals RNAs directly interacting with CTCF in human transformed cell line U2OS
This experiment sought to determine the genome-wide interactome of CTCF in human cells. PAR-CLIP seq for CTCF was performed in U2OS cells in 2 biological replicates
ORGANISM(S): Homo sapiens 
2014-03-18 | E-GEOD-53554 | biostudies-arrayexpress
TranscriptomicsAGO-PAR-CLIP of DG75 and BCBL-1
AGO-PAR-CLIP was employed to identify microRNA binding sites in BCBL-1, a Kaposi's sarcoma-associated herpesvirus (KSHV) infected B-cell line and DG75, a KSHV negative B-cell line as a control. By using our novel computational method (PARma) and differential analysis of PAR-CLIP data, highly accurat...
ORGANISM(S): Homo sapiens 
2013-06-27 | E-GEOD-43909 | 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
TranscriptomicsAdvancing Functional Utility of PAR-CLIP by Quantifying Background Binding to mRNAs and lncRNAs
We developed a method for measuring non-specific background in PAR-CLIP data demonstrating that covalently crosslinked background binding is common, reproducible and apparently universal. Furthermore, we show that quantitative determination of background is essential for identifying targets of weak...
ORGANISM(S): Homo sapiens 
2013-11-07 | E-GEOD-50989 | biostudies-arrayexpress
GenomicsPAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif [PAR-CLIP]
PAPD5 is one of the seven members of non-canonical poly(A) polymerases in human cells. There are previous reports about polyadenylation dependent degradation of pre-ribosomal RNAs and uridylation dependent degradation of histone mRNAs in vivo. In this study, we observed polyadenylation but not polyu...
ORGANISM(S): Homo sapiens 
2012-04-02 | E-GEOD-36987 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide identification of LARP4B binding sites in HEK293 cells
mRNAs are key molecules in gene expression and subject to diverse regulatory events. Regulation is accomplished by distinct sets of trans-acting factors that interact with mRNAs and form defined mRNA-protein complexes (mRNPs). The resulting “mRNP code” determines the fate of any given mRNA and thus ...
ORGANISM(S): Homo sapiens 
2015-05-26 | E-GEOD-69169 | biostudies-arrayexpress
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
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