Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq.
Abstract
Discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets plays a critical role in enabling our understanding of how these RBPs control RNA processing and regulation. 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 contact. By simplifying technical challenges in prior CLIP methods and incorporating the generation of and quantitative comparison against size-matched input controls, the single-end enhanced CLIP (seCLIP) protocol allows for the profiling of these interactions with high resolution, efficiency and scalability. Here, we present a step-by-step guide to the seCLIP method, detailing critical steps and offering insights regarding troubleshooting and expected results while carrying out the ~4-d protocol. Furthermore, we describe a comprehensive bioinformatics pipeline that offers users the tools necessary to process two replicate datasets and identify reproducible and significant peaks for an RBP of interest in ~2 d.
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Linked Datasets (1)
Transcriptome-wide identification of RNA binding protein binding sites using seCLIP-seq
Homo sapiens5 data files
| File | Type | Size |
|---|---|---|
| 4114_CLIP1_S39_L002_R1_001.fastq.gz | RIP-Seq | 684.8 MB |
| 4114_CLIP2_S41_L002_R1_001.fastq.gz | RIP-Seq | 645.2 MB |
| 4114_INPUT1_S38_L002_R1_001.fastq.gz | RIP-Seq | 655.7 MB |
| 4114_INPUT2_S40_L002_R1_001.fastq.gz | RIP-Seq | 629.8 MB |
| SRR15222630.lite | RIP-Seq | 629.8 MB |
Potentially Related Datasets (1)
These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.