Cross-linking immunoprecipitation - Wikipedia
Cross-linking and immunoprecipitation (CLIP, or CLIP-seq) is a method used in molecular biology that combines UV crosslinking with immunoprecipitation in order to identify RNA binding sites of proteins on a transcriptome-wide scale, thereby increasing our understanding of post-transcriptional regulatory networks.
CLIP and complementary methods - Nature Reviews Methods …
2021年3月4日 · To identify the sites bound by a specific RNA-binding protein on endogenous RNAs, cross-linking and immunoprecipitation (CLIP) and complementary, proximity-based methods have been developed.
The Future of Cross-Linking and Immunoprecipitation (CLIP)
Cross-linking and immunoprecipitation (CLIP) serves this purpose by exploiting covalent protein–RNA cross-linking and RNA fragmentation, along with a series of stringent purification and quality control steps to prepare complementary DNA (cDNA) libraries for sequencing.
CLIP-Seq to identify targets and interactions of RNA binding proteins ...
One of the essential tools for studying erasers, writers, and readers is cross-linking immunoprecipitation followed by high-throughput sequencing (CLIP-seq). This method can detect the sites on endogenous RNAs bound by RNA-binding proteins or RNA modifying enzymes.
CLIPSeqTools—a novel bioinformatics CLIP-seq analysis suite
In this study, we present CLIPSeqTools, a novel, highly flexible computational suite that can perform analysis from raw sequencing data with minimal user input. It contains a wide array of tools to provide an in-depth view of CLIP-seq data sets.
CLIPdb: a CLIP-seq database for protein-RNA interactions
2015年2月5日 · CLIP-seq provides higher resolution than previous technologies (e.g., RNA Immunoprecipitation) for identifying protein binding sites on RNAs. Approximately 400 CLIP-seq samples from about 80 publications are publicly available from various model organisms.
Transcriptome-wide identification of RNA-binding protein
2016年3月28日 · Cross-linking and immunoprecipitation (CLIP) provides a generalizable, transcriptome-wide method by which RBP/RNA complexes are purified and sequenced to identify sites of intermolecular...
Genome-Wide Profiling of RNA–Protein Interactions Using CLIP-Seq
UV crosslinking immunoprecipitation (CLIP) is an increasingly popular technique to study protein–RNA interactions in tissues and cells. Whole cells or tissues are ultraviolet irradiated to generate a covalent bond between RNA and proteins that are in close contact.
Towards in silico CLIP-seq: predicting protein-RNA interaction via ...
2023年8月4日 · We present RBPNet, a novel deep learning method, which predicts CLIP-seq crosslink count distribution from RNA sequence at single-nucleotide resolution. By training on up to a million regions, RBPNet achieves high generalization on eCLIP, iCLIP and miCLIP assays, outperforming state-of-the-art classifiers.
RNA Immunoprecipitation (RIP) & Cross-Linking Immunoprecipitation (CLIP)
HITS-CLIP (or CLIP-seq): Stands for high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation, which utilizes in vivo UV crosslinking technologies and next-gen sequencing.