RIP-seq Analysis

RIP-seq Analysis

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CD Genomics uses bioinformatics to provide RIP-seq data analysis and help you reveal the interaction of RNA molecules and RNA binding protein within the whole transcriptome quickly and accurately. Our unique data analysis skills and high-quality data analysis platform will exceed your expectations on personalized data analysis needs.

Introduction of RIP-seq Analysis

RNA immunoprecipitation (RIP) is a powerful method to study the physical association between individual proteins and RNA molecules in vivo. The basic principles of RIP are  similar to those of chromatin immunoprecipitation (ChIP), a largely used tool in epigenetics, but with some important caveats. The approach is based on the use of a specific antibody raised against the protein of interest to pull down the RNA-binding protein (RBP) and target-RNA complexes. Any RNA that is associated with this protein complex will also be isolated and can be further analyzed by polymerase chain reaction-based methods, hybridization, or sequencing.

RIP-Seq combines RIP with the next generation sequencing technology. By analyzing the sequencing data through bioinformatics, we can efficiently reveal the interaction of RNA molecules and RNA binding protein within the whole transcriptome. It is helpful to understand the dynamic process of post-transcriptional regulatory network in organisms. The relevance of RNA-protein interactions in modulating mRNA and noncoding RNA function is increasingly appreciated and several bioinformatics methods have been recently developed to map them.

RIP-Seq sequencing work process. - CD Genomics.Fig 1.RIP-Seq sequencing work process.

Application Field

Identify the interaction network with RNA and RNA binding protein within the whole transcriptome.

Research on the functional mechanism of non-coding RNA.

Analysis of the interaction between RBP and noncoding RNA such as miRNA, lncRNA.

Discover new protein binding sites.

Advantages of CD Genomics

Analysis pipeline specifically for RIP-seq.

Strict data analysis process and strict data quality control ensure accurate and reliable data analysis results.

The data analysis plan can be customized according to actual needs.

CD Genomics Data Analysis Pipeline

RCD Genomics RIP-seq data analysis pipeline - CD Genomics.

Bioinformatics Analysis Content

CD Genomics uses analysis software specially developed for RIP-seq to perform RIP-seq data bioinformatic analysis. We first perform peak calling in the range of the transcriptome, annotate the peak location information of the genome and the sequence information of the peak region, and obtain the relevant genes of the peak based on the annotation information. Finally, differential analysis of the relevant genes is performed.

Data preprocessing Data quality control
Data statistics
Remove adapter
Remove low quality reads
Map to reference genome Comparison rate
Unique comparison rate
Sequencing depth
Distribution of reads on chromosomes
Peak calling analysis and annotation Peak related gene annotation
Peak distribution on gene functional elements
Peak-related gene function enrichment analysis
Motif analysis Perform motif analysis on the complete transcript of peak related genes
Differential peak analysis Difference peak analysis
Difference peak gene annotation
GO enrichment analysis of related genes
KEGG pathway enrichment analysis of related genes
Visualization of results Visual display of analysis results

We will provide appropriate bioinformatic analysis content according to your needs of RIP sequencing data analysis. For more information, please click online inquiry.

How It Works

CD Genomics is a high-tech company specializing in multiomic data analysis. We provide services such as project design, data analysis, and database construction. With a focus on developing breakthrough products and services, we are a pioneer in the biotechnology industry, serving researchers and partners worldwide.

How It Works

CD Genomics provides general analysis and customized analysis of RIP sequencing data analysis. Experienced teams of scientists, researchers, and technicians, we provide fast turnaround, high-quality data reports at competitive prices for worldwide customers. Customers can contact our employees directly and we will respond promptly. If you are interested in our services, please contact us for more detailed information.


  1. Gagliardi M, Matarazzo M R. RIP: RNA Immunoprecipitation [J]. methods in molecular biology, 2016;1480:73-86.
* For Research Use Only. Not for use in diagnostic procedures.
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