ABSTRACT: This experiment aims to globally identify LARP6 binding sites on the transcriptome by performing iCLIP in MDA-MB231 cell lines expressing GFP-LARP6. MDA-MB231 cell lines expressing GFP only were used as controls in the experiment.
Project description:This experiment aimed to identify Nucleolin (Ncl) binding sites on a transcriptome-wide scale, by performing iCLIP in mouse iKras PDAC cells (Ying et al., 2012) transiently transfected with a mammalian expression construct encoding a wild-type (WT) myc-Ncl, a phospho-defective mutant in which S28, S34, S40, and S41 residues were mutated to A, or a phospho-mimicking mutant with these residues mutated to D. Cells transfected with an empty vector (myc-pRK5-DEST) were used as controls in the experiment.
Project description:TDP-43 is an important RNA binding protein. To better understand its binding targets in human neurons, we performed TDP-43 iCLIP on SHSY5Y cells.
Project description:RNA-sequencing data from MDA-MB231 breast cancer cells, U87MG glioblastoma cells, and mouse breast cancer PDX models treated with antisense oligonucleotides targeting exon 2 of TRA2B. Additionally, RNA-sequencing data from MDA-MB231 breast cancer cells and U87MG glioblastoma cells treated with siRNAs targeting TRA2B. RNA-sequencing data from MDA-MB231 breast cancer cells nad U87MG glioblastoma cells treated with antisense oligonucleotides targeting exon 2 of TRA2B.
Project description:Our ChIP resuls suggested that coilin association with U3, snRNA and histone genes might be dependent on coilin-RNA interaction. We used iCLIP of coilin-GFP expressed in HeLa and P19 cell lines at endogenous levels to identify coilin RNA targets and investigate RNA-binding specificity. P19 cells expressing GFP fused to a nuclear localization signal (GFP-NLS) was used as a negative control. iCLIP results revealed that coilin binds several classes of ncRNA including snRNAs, U3 snoRNA and scaRNAs. Interestlignly the majority of coilin targets were intronic snoRNAs, suggesting a novel role of CBs in snoRNA biogenesis. 5 biological replicates from P19 and 2 biological replicates from HeLa cells after UV-crosslinking. Negative control samples prepared from GFP-NLS fusion protein are stored uder accession E-MTAB-747.
Project description:RNA-Seq profiling of triple-negative MDA-MB-231 cell line with know-down of non-canonical WNT signaling receptor Ror1. The MDA-MB231 cells were either transfected with a non-sense control shRNA (shCTL) or with a ROR1 shRNA (shROR1) construct. The objective was to find expression-responsive targets of these perturbations as potential drivers of MDA-MB231 cell invasiveness.
Project description:We analysed the impact of LARP6 depletion on the proteome of actively growing MDA-MB231 breast cancer cells by SILAC. For this purpose, Light (L) SILAC-labelled MDA-MB231 cells were treated with non-targeting control (NT) or two independent LARP6 siRNA (18i & 97i) for 72 hrs, before lysis in 4% SDS, 100mM Tris/HCl pH 7.5. In parallel, Heavy (H)SILAC labelled non-transfected MDA-MB231 cells were grown and lysed similarly. Each L labeled lysate was then mixed with an equal amount of H labelled lysate. Mixing of samples to the same H standard therefore allowed cross-comparison of different siRNA treatments from separate runs.
Project description:Alternative splicing—the production of multiple mRNA isoforms from a single gene—is regulated in part by RNA-binding proteins (RBPs). While the RBPs Tra2? and Tra2? have both been implicated in the regulation of alternative splicing, their relative contribution to this process are not well understood. Here we use iCLIP to identify Tra2? target exons in MDA-MB-231 cells. We find that simultaneous—but not individual—depletion of Tra2? and Tra2? induces substantial shifts in the splicing pattern of endogenous Tra2? target exons identified by iCLIP. We next use RNA-seq following joint Tra2 protein depletion to comprehensively identify Tra2 protein-dependent exons in MDA-MB-231 cells. Endogenous Tra2? binding sites were mapped across the MDA-MB-231 cell transcriptome in biological triplicate iCLIP experiments. RNA-seq was performed using three biological replicates of negative control siRNA treated MDA-MB-231 cells and three biological replicates of TRA2A and TRA2B siRNA treated MDA-MB-231 cells.