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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
TranscriptomicsCLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex
The exon junction complex (EJC) is a central effector of mRNAs fate, linking nuclear processing to mRNA transport, translation and surveillance. Little is known about its transcriptome-wide targets. We used high-throughput sequencing after crosslinking and immunoprecipitation (HITS-CLIP) in human ce...
ORGANISM(S): Homo sapiens 
2012-10-21 | E-GEOD-40778 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide discovery of microRNA binding sites in human brain by Ago2 HITS-CLIP [Ago2-miRNA complexes]
Here, seeking to gain insight into the array of transcripts engaged with miRNAs in human brain, we performed HITS-CLIP to profile transcriptome-wide Ago2:RNA interactions in a panel of eleven post-mortem adult human brain samples harvested from adult motor cortex and cingulate gyrus, regions associa...
ORGANISM(S): Homo sapiens 
2014-01-03 | E-GEOD-52083 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide discovery of microRNA binding sites in human brain by Ago2 HITS-CLIP [Ago2-miRNA-target mRNA complexes]
Here, seeking to gain insight into the array of transcripts engaged with miRNAs in human brain, we performed HITS-CLIP to profile transcriptome-wide Ago2:RNA interactions in a panel of eleven post-mortem adult human brain samples harvested from adult motor cortex and cingulate gyrus, regions associa...
ORGANISM(S): Homo sapiens 
2014-01-03 | E-GEOD-52082 | biostudies-arrayexpress
TranscriptomicsHITS-CLIP reveals key regulators of nuclear receptor signaling in breast cancer.
We used a genome-wide approach (High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation, or HITS-CLIP) to define direct miRNA-mRNA interactions in three breast cancer subtypes (estrogen receptor positive, Her2 amplified and triple negative). Focusing on steroid receptor signal...
ORGANISM(S): Homo sapiens 
2014-08-04 | E-GEOD-57855 | biostudies-arrayexpress
TranscriptomicsElucidation of Transcriptome-Wide MicroRNA Binding Sites in Human Cardiac Tissues by Ago2 HITS-CLIP
We deciphered Ago2:RNA interactions in post-mortem human heart tissues using crosslinking immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to generate the first transcriptome-wide map of miR targeting events in human myocardium, detecting 4000 cardiac Ago2 binding sites across...
ORGANISM(S): Homo sapiens 
2016-08-09 | E-GEOD-83410 | biostudies-arrayexpress
TranscriptomicsDGCR8 HITS-CLIP reveals novel functions for the Microprocessor (CLIP-seq)
The Drosha-DGCR8 complex (Microprocessor) is required for microRNA (miRNA) biogenesis. DGCR8 contains two double-stranded RNA binding motifs that recognize the RNA substrate, whereas Drosha functions as the endonuclease. We have used high-throughput sequencing of RNAs isolated by crosslinking immuno...
ORGANISM(S): Homo sapiens 
2012-07-15 | E-GEOD-39086 | 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
GenomicsHITS-CLIP analysis of FUS in lineage-committed cells.
In the present study, we performed HITS-CLIP analysis for FUS using mouse brain to extensively characterize tits RNA-binding sites and functional roles in RNA metabolisms. We identified preferential binding of FUS to stem-and-loop structures but without any discernible consensus motifs. FUS was pref...
ORGANISM(S): Mus musculus 
2012-07-26 | E-GEOD-37190 | biostudies-arrayexpress
TranscriptomicsArgonaute HITS-CLIP to identify miRNA target sites in the bovine retina
We report identification of 348 high confidence miRNA target sites in 261 genes in the bovine retina Employ Argonaute HITS-CLIP analysis to identify miRNA target sites in the bovine retina
ORGANISM(S): Bos taurus 
2014-09-10 | E-GEOD-59909 | biostudies-arrayexpress
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