Ontology highlight
ABSTRACT:
PROVIDER: PRJNA899006 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:RIP assays to find RNAs interacting with HSC70.1 chaperone of A. thaliana Col0
| PRJEB44090 | ENA
Project description:We report the application of RNA-Seq, m6A-Seq and RIP-Seq to find out YTHDF1 regulate the target genes.
2023-08-21 | GSE228280 | GEO
Project description:We report the application of RNA-Seq, m6A-Seq and RIP-Seq to find out YTHDF1 regulate the target genes.
2023-08-21 | GSE228277 | GEO
Project description:We report the application of RNA-Seq, m6A-Seq and RIP-Seq to find out YTHDF1 regulate the target genes.
2023-08-21 | GSE228274 | GEO
Project description:To explain the possible molecular mechanism underlying the oncogenic roles of IGF2BP3 in EC, we employed RNA immunoprecipitation (RIP) assays to identify the lncRNAs involved in the regulation of IGF2BP3 function. RIP experiments, high-throughput sequencing and data analysis were performed by Seqhealth Tech (Wuhan, China). RIP assays were carried out on Ishikawa cells. The cells were lysed, and the lysis samples for immunoprecipitation reactions were incubated with anti-IGF2BP3 antibody (ab177477, Abcam, USA) or rabbit IgG (Cell Signaling Technology). The library products were enriched, quantified and finally sequenced on the Illumina PE150 platform.One hundred ninety-one candidates as IGF2BP3-interacting lncRNAs were identified in the RIP-seq results.
2022-03-16 | GSE198620 | GEO
Project description:We exploited the methylation genome-scale screening RRBS to correlate the RNA species physically associated with DNMT1 and proximal to the annotated genes to the methylation status of the corresponding loci. Out of 15275 non ambiguous gene loci identified by DNMT1 RIP-Seq, 9436 loci were covered by RRBS. These 9436 loci were clustered according to the fold of specific DNMT1 library peaks enrichment (defined as the ratio of the sum of the area under the curve of specific DNMT1 library peaks covering the gene loci). Genes were then stratified by the expression profile ultimately leading to the epitranscriptome map, a comprehensive map cross-referencing DNMT1-interacting transcripts to (i) DNA methylation and (ii) gene expression profile. Relationship between DNMT1-RNA interactions, DNA methylation and gene expression
2012-12-01 | E-GEOD-32168 | biostudies-arrayexpress
Project description:Neural stem cells (NSCs) in the adult mammalian subependymal zone maintain a glial identity and the developmental potential to generate neurons during the lifetime. Production of neurons from these NSCs is not direct but follows an orderly pattern of cell progression which allows the gradual increase along the neurogenic lineage in the expression of pro-neural factors needed for neuronal specification. In this context, tightly regulated translation of existing transcriptional programs represents a potential mechanism to avoid the critical challenge posed by genes that encode proteins with conflicting functions, i.e. self-renew or differentiate. Here, we identify RNA-binding protein MEX3A as a post-transcriptional regulator of a set of stemness-associated transcripts at critical transitions in the subependymal neurogenic lineage. MEX3A binding to a set of quiescence-related RNAs in activated NSCs is needed for their return to quiescence, playing a role in the long-term maintenance of the NSC pool. Furthermore, it is required for the repression of the same program at the onset of neuronal differentiation. Our data indicate that MEX3A is a pivotal regulator of adult mammalian neurogenesis acting as a translational remodeller.
2023-01-08 | PXD038983 | Pride
Project description:Scaffold Attachment Factor B (SAFB) is a conserved RNA Binding Protein (RBP) that is essential for early mammalian development. However, the RNAs that associate with SAFB in mouse embryonic stem cells have not been characterized. Here, we addressed this unknown using RNA-seq and SAFB RNA immunoprecipitation followed by RNA-seq (RIP-seq) in wild-type mouse embryonic stem cells (ESCs) and in ESCs in which SAFB and SAFB2 were knocked out. The transcript most enriched in SAFB association was the lncRNA Malat1, which contains a series of purine-rich motifs in its 5 end. Beyond Malat1, SAFB predominantly associated with introns of protein-coding genes also through purine-rich motifs. Knockout of SAFB/2 led to down- and upregulation of genes in multiple biological pathways. The nascent transcripts of many downregulated genes associated with high levels of SAFB in wild-type cells, implying that SAFB binding promotes the expression of these genes. Reintroduction of SAFB into double-knockout cells restored gene expression towards wild-type levels, an effect that was again observable at the level of nascent transcripts. Proteomic analyses indicate an enrichment of nuclear speckle-associated, SR proteins in FLAG-tagged SAFB immunoprecipitated samples. Comparison to immunoprecipitates made from FLAG-tagging of another nuclear-enriched RNA-binding protein called HNRNPU (also known as SAF-A) identified both similarities and differences. Perhaps most notably, we observed a stronger enrichment for speckle-associated proteins in SAFB immunoprecipitations and a strong enrichment for paraspeckle-associated proteins in HNRNPU immunoprecipitations. Our findings suggest that among other potential functions in mouse embryonic stem cells, SAFB directly promotes the expression of a subset of genes through its ability to bind purine regions in nascent RNA.
2023-07-20 | PXD038103 | Pride
Project description:RIP-seq analysis of Isw1 interacting transcripts
| PRJEB14710 | ENA