Arraystar (h)MeDIP-seq service with lncRNA promoter analysis offers added benefits to obtain in depth data analyses and annotations of 5mC or 5hmC modifications on both mRNA and lncRNA gene promoters.
• Performance optimized (h)MeDIP methods, rigorous QC process, and high mappable reads
• (hydroxy-)methylation analysis on both mRNA and lncRNA gene promoters
• Standard analysis package with advanced features
• Seamless integration with our lncRNA expression array profiling technology
Differential methylation or hydroxymethylation in lncRNA promoter regions between samples or groups
The differential (hydroxy)methylation in the lncRNA promoter regions ( /- 2000 bp of TSS) is annotated with the reference genome (Fig. 1).
Figure 1. Differentially methylated regions in the lncRNA promoter regions are tabulated with the fold changes , p- and q-values for statistical significance, and genomic annotation.
Combined analysis of (h)MeDIP-seq of lncRNA promoters with lncRNA expression
The epigenetic modification data from (h)MeDIP-seq and the gene expression profiles are combined for integrative analysis. The 5mC or 5hmC differentially modified genes and the differentially expressed genes are hierarchically clustered on the heatmaps, to allow correlation of the changes (Fig. 2).
Figure 2. A combined analysis of hMeDIP-seq and LncRNA expression array profiling, as shown in the clustering heatmaps, to reveal the relationship of hydroxymethylation of lncRNA promoters with the lncRNA gene expression.
Visualization of LncRNA promoter (hydroxy)methylation
The (h)MeDIP-seq data are formatted as compatible WIG files for uploading to genome browsers such as UCSC Genome Browser. The (h)MeDIP signals can be visualized along with genomic features and a wealth of other gene expression, gene regulation, phenotypic tracks from many other sources.
Figure 3. Genome browser visualization of hydroxymethylation peaks from hMeDIP-seq data.
Purified genomic DNA, or frozen tissues, or cell pellets
Please refer to Sample Submission for details in how to get your project started.
1. Genomic DNA isolation (Optional)
2. Genomic DNA QC
3. Immunoprecipitation by anti-5-(hydroxyl-)methylcytosine antibody
4. Sequencing library prep and library QC
5. Sequencing by Illumina platform
6. Data Extraction, Analysis and Summarization