#Iclip experiments protocols rna ip software

#Iclip experiments protocols rna ip software

OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Preprocessing and analysis of LC-MS-based proteomic data. The CRAPome: a contaminant repository for affinity purification–mass spectrometry data. Unbiased RNA-protein interaction screen by quantitative proteomics. Comprehensive analysis of mass spectrometry methods used in proteomics.īutter, F., Scheibe, M., Mörl, M. Quantitative mass spectrometry in proteomics: a critical review. Protocol Exchange (2018).īantscheff, M., Schirle, M., Sweetman, G., Rick, J. RNA-protein interaction detection (RaPID). RNA–protein interaction detection in living cells. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. An improved smaller biotin ligase for BioID proximity labeling. Probing nuclear pore complex architecture with proximity-dependent biotinylation. Capture hybridization analysis of RNA targets (CHART). Systematic discovery of Xist RNA binding proteins. RNA aptamers for the MS2 bacteriophage coat protein and the wild-type RNA operator have similar solution behaviour.

A versatile tandem RNA isolation procedure to capture in vivo formed mRNA-protein complexes. Quantitative profiling of in vivo–assembled RNA-protein complexes using a novel integrated proteomic approach. A protocol for PAIR: PNA-assisted identification of RNA binding proteins in living cells. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. RAP-MS: a method to identify proteins that interact directly with a specific RNA molecule in cells. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. The genomic binding sites of a noncoding RNA. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Formaldehyde crosslinking: a tool for the study of chromatin complexes. Photocross-linking of nucleic acids to associated proteins. fCLIP-seq for transcriptomic footprinting of dsRNA-binding proteins: lessons from DROSHA. Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genomics Proteomics Bioinformatics 12, 72–78 (2014).īeckmann, B. Genome-wide mapping of cellular protein-RNA interactions enabled by chemical crosslinking. Utility of formaldehyde cross-linking and mass spectrometry in the study of protein-protein interactions. The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer. Control of somatic tissue differentiation by the long non-coding RNA TINCR. RNA-protein analysis using a conditional CRISPR nuclease. An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins. RNA-based affinity purification reveals 7SK RNPs with distinct composition and regulation. Tobramycin affinity tag purification of spliceosomes. In RNA–Protein Complexes and Interactions (ed. Detecting RNA–protein interaction using end-labeled biotinylated RNA oligonucleotides and immunoblotting. Ribonomic approaches to study the RNA-binding proteome. Metabolic enzymes enjoying new partnerships as RNA-binding proteins. Comprehensive identification of RNA-binding domains in human cells. Conserved mRNA-binding proteomes in eukaryotic organisms. Utilization of RNA metabolic labeling to comprehensively capture the RNA–protein interactome independent of RNA polyadenylation. Transcriptome-wide discovery of coding and noncoding RNA-binding proteins. Comprehensive poly(A) RNA–protein interactome capture performed in HeLa cells. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. A brave new world of RNA-binding proteins. In RNA Sequence, Structure and Function: Computational and Bioinformatic Methods (eds. Re, A., Joshi, T., Kulberkyte, E., Morris, Q. The human RNA-binding proteome and its dynamics during translational arrest. Purification of cross-linked RNA-protein complexes by phenol-toluol extraction. Long noncoding RNAs: cellular address codes in development and disease. Clinical severity and thermodynamic effects of iron-responsive element mutations in hereditary hyperferritinemia-cataract syndrome. From birth to death: the complex lives of eukaryotic mRNAs.