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Reduced Representation Bisulfite Sequencing (RRBS)


Reduced Representation Bisulfite Sequencing (RRBS) has emerged as a cost-effective and efficient alternative to Whole Genome Bisulfite Sequencing (WGBS) in DNA methylation research. While WGBS provides comprehensive insights by examining the entire genome at single base resolution, its high cost can be a limiting factor. RRBS strategically mitigates this challenge by selectively analyzing a representative portion of the genome. This methodology relies on the enrichment of CpG island-rich regions by MspI cleavage followed by size selection of 200-500/600 bps fragments. Consequently, only regions proximal to CpG islands are sequenced, while those with distant CpG islands are excluded from the analysis. This process, combined with bisulfite sequencing, allows for high-resolution detection of DNA methylation, and the sequencing approach, PE150, focuses specifically on the ends of the inserts rather than the middle, increasing the efficiency of methylation profiling. The RRBS is an invaluable tool that enables cost-effective DNA methylation research and advances knowledge of epigenetic mechanisms.

Service Details


Demo Result

Featured publications

Service Features

●  Requires a reference genome.

●  Lambda DNA is used to monitor bisulfite conversion efficiency.

●  MspI digestion efficiency is also monitored.

●  Sequencing on Illumina NovaSeq.

Service Advantages

●  Cost-effective and efficient alternative to WGBS: enabling the analysis the be carried out at a lower cost and with lower sample requirements.

●  Complete platform: provide one-stop excellent service from sample processing, library construction, and sequencing to bioinformatics analysis.

●  Extensive Expertise: with RRBS sequencing projects successfully completed across a diverse range of species, BMKGENE brings over a decade of experience, a highly skilled analysis team, comprehensive content, and excellent post-sales support.

●  Possibility to join with transcriptomics analysis: allowing for the integrated analysis of WGBS with other omics data such as RNA-seq.

Service Specifications


Sequencing Strategy

Recommended data output

Quality control

MspI digested and Bisulfite treated library

Illumina PE150



Bisulfite conversion >99%

MspI cutting efficiency > 95%

Sample Requirements


Concentration (ng/µL)

Total amount (µg)


Genomic DNA



Limited degradation or contamination

Service Work Flow

sample delivery

Sample delivery

Library Preparation

Library construction



Data analysis

Data analysis

After sale Services

After-sale services

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    Includes the following analysis:

    ● Raw sequencing quality control;

    ● Mapping to reference genome;

    ● Detection of 5mC methylated bases and motif identification;

    ● Analysis of methylation distribution and sample comparison;

    ● Analysis of Differentially Methylated Regions (DMRs);

    ● Functional annotation of genes associated to DMRs.

    Quality control: digestion efficiency (in genome mapping)



    Quality control: bisulfite conversion (in methylation info extraction)



    Methylation map: 5mC methylation genome-wide distribution



    Sample comparison: Principal Component Analysis



    Differentially Methylated Regions (DMRs) analysis: heatmap






    Explore the research advancements facilitated by BMKGene’s whole genome bisulfite sequencing services through a curated collection of publications.

    Li, Z. et al. (2022) ‘High-fidelity reprogramming into Leydig-like cells by CRISPR activation and paracrine factors’, PNAS Nexus, 1(4). doi: 10.1093/PNASNEXUS/PGAC179.

    Tian, H. et al. (2023) ‘Genome-wide DNA methylation analysis of body composition in Chinese monozygotic twins’, European Journal of Clinical Investigation, 53(11), p. e14055. doi: 10.1111/ECI.14055.

    Wu, Y. et al. (2022) ‘DNA methylation and waist-to-hip ratio: an epigenome-wide association study in Chinese monozygotic twins’, Journal of Endocrinological Investigation, 45(12), pp. 2365–2376. doi: 10.1007/S40618-022-01878-4.

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