DNA methylation is an indispensible epigenetic modification required for regulating the expression of genomes. In mammals, it occurs predominantly at CpG dinucleotides and is involved in diverse processes such as development, genomic integrity, X-inactivation and imprinting. Furthermore, perturbed DNA methylation is a hallmark of many human diseases, including cancers.
Whole genome DNA methylation profiling has been advanced recently by the application of high throughtput DNA sequencing technology. MeDIP-sequencing (Methylated DNA immunoprecipitation in conjunction with high throughput sequencing) allows scientists to create high resolution methylation profiles of DNA methylation state on a genome-wide scale.
MeDIP-sequencing Service at Arraystar
With Genome Analyzer IIx, Arraystar offers integrated MeDIP-sequencing service from MeDIP-sequencing library preparation to comprehensive data analysis.
Highlight Features of Arraystar MeDIP-Sequencing Service
1. Optimized library preparation to achieve high sensitivity and reliability
2. Visualization of specific regions of DNA methylation
3. Digital quantification of DNA methylation level
1. Optimized Library Preparation to Achieve High Sensitivity and Reliability
MeDIP is capable of enriching not only CpG islands, but also CpG island shores, which are important considering their importantce as DMRs in phenotypic plasticity. Our optimized library preparation makes it possible to analyze as little as 1 ug or less of starting genomic DNA. Strict quality assessment of MeDIP and sequencing library (Figure 1) ensures the high quality of the MeDIP-sequencing library.
Fig 1. Optimized workflow of MeDIP-sequencing library preparation
2. Visualization of DNA Methylation Profiles
We provide whole genome DNA methylation profiles at 50 bp resolution, which can be visualized in UCSC genome browser. Therefore, any region of interest (ROI) can be directly visualized, compared and investigated (Figure 2).
Fig 2. MeDIP-sequencing signals at PDE4DIP gene locus. Up panel (A) shows the MeDIP signals at PDE4DIP gene locus, while detailed DNA methylation signals of two CpG islands in this region are shown in the two charts below (B, C).
3. Digital Quantification of DNA Methylation
To further quantify the DNA methylation level of any specific region, we use MeDIP-score (the number of extended reads per kb in the genome) to quantify methylation level of any region of interest (ROI) in the genome. We provide not only whole genome DNA methylation profiles, but also the methylation profiles of specific regions, such as CpG islands (promoter, intragenic, downstream and intergenic CpG islands), promoters (HCP, ICP, LCP), CpG island shores, gene bodies, genomic repetitive regions, CTCF and enhancers.
Fig 3. Digital quantification of CpG island (Chr1:156186237-156186647). The methylation level of the CGI is quantified by MeDIP-score, which is 658 reads/kb.
Description of Services
Please refer to Sample Submission for details in how to get your project started.
2. DNA Fragmentation and Validation
3. Sequencing Adapter Ligation
4. Obtaining Methylated DNA Fragments by MeDIP
5. Adapter-Mediated PCR
6. Quality Assessment of MeDIP and Sequencing Library
7. Cluster Generation on Cluster Station
8. Sequencing by Genome Analyzer IIx
9. Data Extraction, Analysis and Summarization