MeDIP-chip combines methylated DNA immunoprecipitation (MeDIP) with microarray technology to give a detailed profile of genome-wide methylation, and provides insight into the mechanisms of DNA methylation. We provide services for methylation arrays designed by Arraystar, Roche-Nimblegen and Agilent. The methylation arrays most often selected by our customers are CpG island/promoter microarrays, promoter microarrays, and microRNA DNA methylation microarrays.
Recent Publications Citing Our MeDIP-chip Service
Long lasting alterations to DNA methylation and ncRNAs may underlie the effects of fetal alcohol exposure.
Benjamin I. Laufer, et al. Disease Models & Mechanisms, 2013
Arraystar DNA Methylation Arrays
LncRNA promoter microarrays are designed to investigate the epigenetic modifications and transcription factor binding sites within LncRNA promoter regions, and uncover other biologically significant genomic regions. These regions include, but are not limited to, mRNA promoters, miRNA promoters, H3K4-K27 bivalent domains, CpG islands and CpG island shores.
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Microarray |
Species |
Array Format |
Coverage |
|
Arraystar Human LncRNA Promoter Array V2.0 |
Human |
1*1M |
28,801 LncRNA promoters (-2.2kb ~ +500bp)
26,109 mRNA promoters (-2.2kb ~ +500bp)
1,595 miRNA promoters (-15kb ~ mature miRNA)
15,156 CpG islands, 30,312 CpG island Shores, 5,273 K4-K27 bivalent domain regions, 481 UCR and 4 Hox cluster regions |
microRNA Genome DNA Methylation microarrays are designed to profile miRNA associated DNA methylation patterns.
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Microarray |
Species |
Array Format |
Coverage |
|
microRNA Genome DNA Methylation Array |
Human |
3*720K |
1,426 miRNA promoters (-40 kb ~ +15 kb of mature miRNA)
1,749 host gene promoters (-8 kb ~ 3 kb of TSS)
2,716 CpG islands nearby (-3 kb ~ + 3 kb of CpG island) |
Roche-Nimblegen DNA Methylation Arrays
CpG Island and Promoter microarrays are designed to analyze specific regulatory elements of the genome, such as gene promoters, microRNA promoters and CpG islands. The ultra-high density 2.1 million arrayscan even detect the genome-wide methylation status of regulatory elements (such as enhancers) located far from promoters and CpG islands.
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Microarray |
Species |
Array Format |
Coverage |
|
Multiplex HG18 CpG Promoter |
Human |
3 * 720K |
22,532 promoters: -2.44kb ~ +0.61kb
27,728 CpG islands |
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Multiplex MM9 CpG Promoter |
Mouse |
3 * 720K |
20,404 promoters : -2.96kb ~ +0.74kb
15,980 CpG islands |
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Multiplex RN34CpG Promoter |
Rat |
3 * 720K |
15,287 promoters: -3.88kb ~ +0.97kb
15,790 CpG islands |
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Mouse DNA Meth 2.1M Deluxe
Pro Arr |
Mouse |
1 * 2.1M |
22,425 gene promoters: -8.2kb ~ +3kb,
16,002 CpG islands,
510 miRNA promoters(-20kb ~through mature transcript) |
Description of Services
Our team has vast experience performing MeDIP-chip on many sample types, such as FFPE (Formalin-Fixed, Pariffin-Embeded), serum, and plasma. Just send us your samples, and we'll do the rest! (Please refer to the Sample Submission Guidelines to help you start your project).
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Option A
(MeDIP DNA submitted) |
Option B
(DNA submitted) |
Option C
(sample submitted) | |
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v | ||
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v |
v | ||
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Sonication |
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v |
v | |
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v |
v | ||
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IP |
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v |
v | |
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v |
v |
v | ||
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Amplification |
v |
v |
v | |
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Labeling |
v |
v |
v | |
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Array hybridization |
v |
v |
v | |
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Standard data analysis |
v |
v |
v | |
* For quotations and inquiries, please specify the type of service that you need: Option A, Option B or Option C.
Arraystar's bioinformatics team has extensive experience in analyzing MeDIP-chip data. We provide two levels of analysis: standard and advanced.
Standard Data Analysis
Customers choosing Standard Data Analysis receive:
• Raw data files derived from the NimbleScan software or Agilent GeneSpring software
• Defferentially Enriched Peak (DEP) analysis
• Summary Report
• Analysis Report Files in GFF format (Genome annotation file, Scaled Log2-ratio Data, P-value Data, Peaks Data, Multi-sample comparison)
The overall promoter CpG content is an excellent predictor of transcriptional repression. Arraystar's bioinformatics team is expert at analyzing MeDIP-chip data. Our unique MeDIP-chip analysis determines the CpG methylation state of mammalian gene promoters (Table 1). The degree of CpG methylation at promoters falls into three classes: High-CpG density promoters (HCP), low-CpG density promoters (LCP) and intermediate-CpG-density promoters (ICP), based on the CpG ratio, GC content and the length of the CpG-rich region.
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Table 1. Results of a MeDIP-chip experiment that uncovered genes whose promoters contain methylated CpG islands. . Each gene is listed in the column on the left. The promoter type (LCP, ICP, or HCP) is indicated in the column highlighted by the blue box.
Advanced Data Analysis
In addition to the Standard Data Analysis, customers choosing Advanced Data Analysis receive:
• Identification of Differentially Methylated Regions (DMRs)
DMRs represent regions of the genome that display significant differences in DNA methylation levels among various cell and tissue types, disease states such as cancers, therapeutic treatments, etc. DMRs are associated with diverse regulatory roles and can serve as epigenetic biomarkers for diagnosis, prognosis and treatment options in clinical settings, as well as for drug design. Arraystar's Advanced Data Analysis uses the most sophisticated analytical methods available for using MeDIP data to identify DMRs.Some examples of DMR results from MeDIP are given in Tables 2 and 3.
1) DMRs in Promoter Region
Table 2. Differentially Methylated Regions in Promoters. The columns in the "dmr_attribution" section (red rectangle) display the differences in methylation status at a given locus between 2 different experimental conditions (represented by "Group A" and "Group B". You can find detailed information of the DMRs in this table, including coordinates, length, methylation status and annotations of the related genes.
2) DMRs in CpG Island region
Table 3. Differentially Methylated Regions in CpG islands. The columns in the "dmr_attribution" section (red rectangle) display the differences in methylation status at a given locus between 2 different experimental conditions (represented by "Group A" and "Group B". You can find detailed information of the DMRs in this table, including coordinates, length, methylation status and annotations of the CpG islands.
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