Introduction to RNA Immunoprecipitation Sequencing (RIP-seq)
RIP-seq (RNA Immunoprecipitation Sequencing) is a powerful technique used to study RNA molecules that are associated with specific RNA-binding proteins (RBPs). It allows researchers to study the interactions between proteins and RNA on a genome-wide scale, shedding light on how RBPs regulate gene expression, RNA splicing, stability, localization and translation.
RIP-seq provides a comprehensive overview of the RNAs bound by a specific protein across the entire transcriptome and can detect RNA-protein interactions with high sensitivity. Its versatility means it can be applied to a variety of RNA types, including coding and non-coding RNAs. RIP-seq can also be used along with other techniques such as ChIP-seq and ATAC-seq to gain further multi-omics insights into biological processes.
Applications of RNA Immunoprecipitation Sequencing (RIP-seq):
RIP-seq is widely used in the field of RNA biology and gene regulation. Its key applications include:
- Identifying RNA Targets of RNA-Binding Proteins: RIP-seq allows researchers to map the RNAs bound by specific RBPs, enabling the identification of their regulatory targets. These targets may include mRNAs and/or non-coding RNAs (ncRNAs).
- Understanding RNA-Protein Interactions in Development and Diseases:RIP-seq can be used to investigate how RBPs regulate RNA processing during embryonic development, cell differentiation and diseases such as cancers.
- Characterizing functions of ncRNAs: RIP-seq can be used to study non-coding RNAs (ncRNAs) bound to specific RBPs, providing insights into their regulatory functions.
Benefits of Novogene’s RIP-seq service:
- Extensive Experience: Novogene has experience in sequencing enriched RNA derived from RIP-seq, CLIP-seq, PAR-CLIP-seq, and MeRIP-Seq/m6A-seq assays.
- High-Quality Data: We deliver high-quality sequencing data that meets leading industry standards. Rigorous quality control (QC) checks are performed at each stage including sample QC, library QC and data QC.
- Bioinformatics Support: We provide comprehensive bioinformatics support and utilize industry-standard MACS2 software and other pipelines with the latest version. Our bioinformatics report is complete with motif prediction, peak annotation, and functional analysis and associated publication-ready figures. Customized bioinformatics support is also available.
- Fast Turnaround Times: Our sequencing labs are located near you, in Germany and the UK, allowing for reduced shipping times. With our large sequencing capacity and automated and streamlined workflows, we ensure that you receive your data promptly without compromising on quality.
- Customer Service System (CSS): Novogene’s Customer Self Service System (CSS) is an online project management portal that streamlines project management and provides direct access to all your sequencing projects in one place. You can view your sequencing project(s), track their progress, access reports, collaborate with your team members and obtain other useful information at one place.
Immunoprecipitation Sequencing Service Flyer
IP-seq is used to study the interaction between proteins and nucleic acids by sequencing the protein-binding motifs within DNA and RNA. Depending on the nucleic acid enriched, it can include chromatin immunoprecipitation (ChIP) and RNA immunoprecipitation (RIP). Novogene takes DNA or RNA fragments enriched by antibodies specific to the protein of interest, maps them against reference genomes and analyses to call peaks. Our service delivers high quality data, publication-ready analysis results, and personalised pipelines.
On-demand Webinar
A Beginner’s Guide to Next Generation Sequencing Solutions for Epigenetics Research
In this webinar, we will showcase Novogene’s diverse sequencing solutions for epigenetics research, including techniques to detect DNA methylation such as Whole Genome Bisulphite Sequencing and EM-seq, determining chromatin accessibility using ATAC-seq, and studying histone modifications (e.g., ChIP-seq), among others. We will delve into the underlying principles of these technologies, explore their various applications, and outline the workflows and analysis pipelines used to achieve comprehensive epigenetic insights.
We will talk about myriad microbial sequencing options such as microbial whole genome sequencing, metagenomics, and metatranscriptomics. We will also discuss recent advances in the field such as the applications of long-read sequencing and highlight Novogene’s diverse microbial sequencing solutions to aid your research.
Learning Objectives:
- Discover sequencing solutions tailored for epigenetics research
- Understand the principles and applications of the various NGS solutions for epigenetics research
- Gain insight into the workflows and bioinformatics analysis pipelines of Novogene’s epigenetics solutions.
RIP-seq Specifications: RNA Sample Requirements
| Sample Type | Required Amount | Volume | Concentration | Fragment Size |
| Enriched RNA Sample | ≥ 20 ng | ≥ 10 μL | ≥ 2 ng/ μL | Fragments longer than 80 nt |
Note: We accept purified/enriched RNA samples only. Sample amounts are listed for reference only. Please don’t hesitate to reach out to us for detailed information or customized requests.
RIP-seq Specifications: Sequencing and Analysis
| Sequencing Platform | Illumina NovaSeq X Plus |
| Read Length | Paired-end 150bp |
| Recommended Data Amount | ≥ 20 million read pairs per sample for the species with a reference genome |
| Content of Data Analysis |
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Note: Sequencing parameters and analysis contents displayed are only for reference. Please contact us for detailed information.
Project Workflow of Novogene’s RIP-seq service:
We accept purified/enriched RNA samples for processing, and follow with Novogene’s RIP-seq service which comprises of four steps, including sample QC, DNA library preparation, Illumina PE150/SE50 sequencing and data analysis using bioinformatics pipelines. From RNA sampling to sequencing the library, every step can potentially impact the quality and quantity of data output, directly influencing the results of the subsequent bioinformatics analysis. Novogene performs rigorous checks at every stage, including sample quality control, library quality control and sequencing data quality control, to ensure the highest quality, accuracy and reliability of the sequencing data delivered to our customers.
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Genome-wide Distribution of Peaks
The number of peaks mapping to the chromosome and its distribution reflect the distribution of the protein binding sites.
Note:
The X-axis is the number of peaks in the chromosome. The Y-axis shows the chromosome numbers. Every blue line represents a peak.
Motif Analysis
Systematic motif analysis is extremely encouraging and promising to comprehend the novel mechanisms in RNA trafficking and sorting as well as in other RNA applications. Motif, or conserved sequence, is shared by multiple binding sites in RNA.
Note:
The figure uses a sequence logo to illustrate the base bias in different positions in the binding sites of a Motif.
Peak Distribution in the Functional Gene Regions
Distribution of peaks in the different functional areas.
Note:
The X-axis represents different functional areas, and Y-axis represents the ratio of the peak in the functional region to the total peaks. The number on the top of the functional region represents the peak number.
*Please contact us to get the full demo report.
