MeDIP-chip Service

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We perform highly optimized MeDIP and profile the IP enriched DNA using arrays designed by Arraystar for genomic features in epigenetic regulation: coding and noncoding gene promoter regions, CpG islands/shores, differentially methylated regions (DMR) and Blocks universally altered in solid tumors.

Arraystar Epigenetic Arrays

Microarray Species Format Coverage
Arraystar Human RefSeq Promoter Array Human 4*180K 23,148 RefSeq promoters (-1,300 bp ~ 500 bp of TSS)
Arraystar Mouse RefSeq Promoter Array Mouse 4*180K 22,327 RefSeq promoters (-1,300 bp ~ 500 bp of TSS)
Arraystar Rat RefSeq Promoter Array Rat 4*180K 15,987RefSeq promoters (-1,300 bp ~ 500 bp of TSS)
Arraystar Human ncRNA Promoter Array Human 4*180K 27,248 lncRNA promoters (-1,300 bp ~ 500 bp of TSS) 
Arraystar Mouse ncRNA Promoter Array Mouse 4*180K 18,552 lncRNA promoters (-1,300 bp ~ 500 bp of TSS)
Arraystar Human Cancer DMR Array  Human 4*180K 12,113 DMRs and nearby 11,380 CpG islands and shores
Arraystar Human Cancer Block Array Human 4*180K 7,088 blocks containing 2,554 mRNA, 8,481 lncRNA and 463 miRNA genes

Service NameFormatPrice
MeDIP-chip Service 4*180K

Arraystar's bioinformatics team has extensive experience in analyzing MeDIP-chip data. We provide our customers with thorough, comprehensive data analysis, including:

•  Methylation Enrichment Peak (EP) finding

•  Defferentially Enriched Peak (DEP) analysis

• The promoters are annotated 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, which is an excellent predictor of transcriptional repression. 

MeDIP-chip-1

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.

• Differentially methylated region analysis by ROI (Advanced analysis with extra fees applied)

MeDIP-ROI

Table 2. Differentially methylated region of interest between two groups.

Arraystar 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).

 

Option A

(MeDIP DNA submitted)

Option B

(DNA submitted)

Option C

(sample submitted)

DNA Isolation

 

 

v

gDNA QC

 

v

v

MeDIP

Sonication

 

v

v

Sheared DNA QC

 

v

v

IP

 

v

v

Quality assessment of MeDIP

v

                 v

v

Amplification

v

v

v

Labeling

v

v

v

Array hybridization

v

v

v

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.

MSC Transplantation Improves Osteopenia via Epigenetic Regulation of Notch Signaling in Lupus. Shiyu Liu, et al. Cell Metabolism, 2016

Long-term parental methamphetamine exposure of mice influences behavior and hippocampal DNA methylation of the offspring. Y Itzhak, et al. Molecular Psychiatry, 2014

TFIIS. h, a new target of p53, regulates transcription efficiency of pro-apoptotic bax gene. JM Liao, et al. Scientific Reports, 2016

Epigenetic inactivation of the CpG demethylase TET1 as a DNA methylation feedback loop in human cancers. Li L, et al. Scientific reports, 2016

Characterization of the nasopharyngeal carcinoma methylome identifies aberrant disruption of key signaling pathways and methylated tumor suppressor genes. Li L, et al. Epigenomics, 2014

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

Sox9 transcriptionally regulates Wnt signaling in intestinal epithelial stem cells in hypomethylated crypts in the diabetic state. Huang C Z, et al. Stem Cell Research & Therapy, 2017

Increased 5-hydroxymethylation levels in the hippocampus of rat extinguished from cocaine self-administration. Sadakierska-Chudy A,  et al. Hippocampus, 2017

DNA methylation differences in monozygotic twin pairs discordant for schizophrenia identifies psychosis related genes and networks. Castellani CA, et al. BMC Med Genomics, 2015

Dietary Chromium Restriction of Pregnant Mice Changes the Methylation Status of Hepatic Genes Involved with Insulin Signaling in Adult Male Offspring. Zhang Q,  et al. PLOS ONE, 2017

Olanzapine-induced methylation alters cadherin gene families and associated pathways implicated in psychosis. MG Melka, et al. BMC Neuroscience, 2014

Epigenetic modification of TLE1 induce abnormal differentiation in diabetic mice intestinal epithelium. Xu J,et al. Molecular and Cellular Biochemistry, 2017

Genome-Wide DNA Methylation in Mixed Ancestry Individuals with Diabetes and Prediabetes from South Africa. Matsha T E, et al. International Journal of Endocrinology, 2016

Olanzapine-induced DNA methylation in the hippocampus and cerebellum in genes mapped to human 22q11 and implicated in schizophrenia. MG Melka, et al. Psychiatric genetics, 2014