Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA226644 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptome-wide discovery of microRNA binding sites in human brain by Ago2 HITS-CLIP [Ago2-miRNA complexes]
| PRJNA226645 | ENA
Project description:Transcriptome-wide discovery of microRNA binding sites in human brain by Ago2 HITS-CLIP (CLIP-Seq)
| PRJNA222996 | ENA
Project description: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 >2200 target transcripts.
2016-08-09 | GSE83410 | GEO
Project description: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 >2200 target transcripts. Profiling AGO2-associated RNAs in cardiac tissues obtained from 6 donors with heart diseases of differing etiologies
2016-08-09 | E-GEOD-83410 | biostudies-arrayexpress
Project description:To estimate transcripts levels in P13 mouse neocortex. MicroRNAs (miRNAs) play critical roles in the regulation of gene expression. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. We used HITS-CLIP to covalently crosslink native Argonaute (Ago) protein-RNA complexes in mouse brain. This produced two simultaneous datasets—Ago-miRNA and Ago-mRNA binding sites—that were combined with bioinformatic analysis to identify miRNA-target mRNA interaction sites. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Here we include the expression data obtained from dissected P13 mouse neocortex. These data are used for in silico CLIP simulation for normalization of Ago HITS-CLIP tags and also for selecting transcripts expressed in P13 mouse cortex.
2009-05-30 | GSE16338 | GEO
Project description:In vivo microRNA-target interactions from adult mouse cortex were identified with CLEAR-CLIP, a modified AGO HITS-CLIP approach that allows direct ligation of microRNA and target within purified, endogenous AGO-RNA complexes.
2019-06-14 | GSE104051 | GEO
Project description: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 GSE21577: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: miRNA inhibition data GSE21918: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: sequencing data Refer to individual Series
2010-04-29 | E-GEOD-21578 | biostudies-arrayexpress
Project description:Argonaute (Ago) proteins interact with various binding partners and play a pivotal role in microRNA (miRNA)-mediated silencing pathways. By utilizing immunoprecipitation followed by mass spectrometry to determine cytoplasmic Ago2 protein complexes in mouse embryonic stem cells (mESCs), we identified a putative RNA-binding protein FAM120A (also known as OSSA/C9ORF10) as an Ago2 interacting protein. Individual nucleotide resolution Cross-Linking and ImmunoPrecipitation (iCLIP) analysis revealed that FAM120A binds to homopolymeric tracts in 3´ UTRs of about 2,000 mRNAs, particularly poly(G) sequences. Comparison of FAM120A iCLIP and Ago2 iCLIP reveals that greater than one-third of mRNAs bound by Ago2 in mESCs are co-bound by FAM120A. Furthermore, such FAM120A-bound Ago2 target genes are not subject to Ago2-mediated target degradation. Reporter assays suggest that the 3´ UTRs of several FAM120A-bound miRNA target genes are less sensitive to Ago2-mediated target repression than those of FAM120A-unbound miRNA targets and FAM120A modulates them via its G-rich target sites. These findings suggest that Ago2 may exist in multiple protein complexes with varying degrees of functionality.
2019-07-09 | GSE128264 | GEO
Project description:microRNAs (miRNAs) are essential components of gene regulation, but identification of miRNA targets remains a major challenge. Most target prediction and discovery relies on perfect complementarity of the miRNA seed to the 3’ untranslated region (UTR). However, it is unclear to what extent miRNAs target sites without seed matches. Here, we performed a transcriptome-wide identification of the endogenous targets of a single miRNA—miR-155—in a genetically controlled manner. We found that approximately forty percent of miR-155-dependent Argonaute binding occurs at sites without perfect seed matches. The majority of these non-canonical sites feature extensive complementarity to the miRNA seed with one mismatch. These non-canonical sites confer regulation of gene expression albeit less potently than canonical sites. Thus, non-canonical miRNA binding sites are widespread, often contain seed-like motifs, and can regulate gene expression, generating a continuum of targeting and regulation. Argonaute (AGO) HITS-CLIP Libraries generated from wild type and miR-155 knockout activated T cells. AGO HITS-CLIP libraries were generated from activated wild type and miR-155 knockout T cells with two different 3' linkers. Libraries were generated and sequenced with an 11nt index read that contained both a 5nt multiplexing index and a 6nt degenerate barcode. Files have been demultiplexed and the 6nt degenerate barcode has been appended as the first 6 nucleotides of the read.
2012-11-09 | E-GEOD-41285 | biostudies-arrayexpress