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Homeobox Genes DNA Methylation PCR Array

NOTE: To access content of the new EpiTect Methyl II PCR Arrays (After May 25, 2012), please click here.
Please NOTE: The new EpiTect Methyl II PCR Array System was introduced effective May 25, 2012. It has replaced the EpiTect Methyl qPCR Array System, with the older system set for discontinuation December 1, 2012.

Human Mouse Rat Signature Panel Rat Complete Panel
Rat Homeobox Genes DNA Methylation PCR Array, Complete Panel
MeAR-8560 (4 × 96-well)
MeAR-3560 (384-well)
The Rat Homeobox Genes EpiTect Methyl Complete qPCR Arrays profile the methylation status of 96 gene promoters involved in multi-cellular organism development. HOX genes encode a group of homeodomain-containing transcription factors, initially described as controlling segmental patterning during development. Recently, their importance has been reemphasized by stem cell and cancer researches. Although these HOX genes have been grouped according to their established roles in multi-cellular organism development, their true function in cellular systems is waiting to be discovered. Profiling cell or tissue samples with these arrays will correlate CpG island methylation status with biological phenotypes. The results also provide insights into the molecular mechanisms and biological pathways behind differentiation and development or oncogenesis. With a simple restriction enzyme digestion and real-time PCR on a 96- or 384-well instrument, research studies can analyze the DNA methylation status of 96 different homeobox genes with the EpiTect Methyl Complete qPCR Arrays.

The EpiTect Methyl qPCR Arrays are intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.

Both 96-well (duplicate set of four arrays) and 384-well formats are available.

The EpiTect Methyl qPCR Arrays use the MethylScreen™ Technology provided under license from Orion Genomics, LLC.

User Manual


Functional Gene Grouping How It Works Manual & Resources Reagents & Software

Anatomical Structure Morphogenesis: Lbx1, Onecut1, Prrx1, Prrx2, Six4.

Organ Morphogenesis: Cdx2, Isl1, Lhx1, Hoxc4, Meis2, Nkx2-8, Nkx6-2, Pitx2, Pitx3, Prox1, Six6.

Body Pattern Formation: Emx2, Hhex, Hipk1, Hoxa10, Hoxa2, Hoxc4, Hoxc5, Hoxd10, Irx3, Lhx2, Pbx1, Pbx2, Pitx2, Rax, Six3, Tgif1.

Ectoderm Development: Prox1, Vax2.

Mesoderm Development: Lhx2.

Endoderm Development: Hnf1b, Irx2, Irx3, Nkx2-1.

Brain & Nervous System Development:
Brain Development: Alx1, Barhl1, Emx2, Hmx3, Hnf1b, Lhx2, Lhx5, Lhx6, Lhx8, Msx1, Nkx2-1, Pou3f1, Rax, Six3, Zeb2.
Nervous System Development: Arx, Barhl2, Dbx1, Dlx5, Hoxd10, Lbx1, Lhx1, Lhx2, Pbx3, Phox2a, Pou3f3, Prrxl1, Shox2, Uncx, Zeb2.

Skeletal Development: Alx4, Dlx3, Dlx5, Hoxa10, Hoxa2, Hoxc4, Hoxd10, Msx2, Pitx1, Shox2.

Muscle Development: Hopx, Irx4, Msx1, Sirt2, Six1.

Other HOX Genes Involved In Multicellular Organismal Development: Barx1, Dlx4, Hoxa1, Hoxa9, Hoxb3, Hoxb4, Hoxb7, Hoxb9, Hoxc12, Isl2, Lbx2, Lmx1a, Meis1, Nkx3-1, Otx1, Pitx1, Vax1, Vsx1.

HOX Genes Involved In Cell Differentiation: Arx, Barhl2, Emx2, Hhex, Hlx, Hnf1b, Hopx, Lbx1, Lhx1, Lhx2, Lhx8, Mixl1, Nkx2-1, Nkx6-1, Nkx6-2, Onecut1, Phox2a, Pou3f1, Pou3f2, Prrxl1, Satb1, Tgif1, Uncx.

Other Genes: Adnp2, Hmx1, Hoxd4, Irx6, Meis3, Pbx4, Phtf2, Sirt3, Sirt5, Sirt7, Six5, Tshz3, Zfhx2.


Functional Gene Grouping How It Works Manual & Resources Reagents & Software
  "If you have access to a real-time PCR instrument, you can analyze the methylation status of multiple genes at the same time using the EpiTect Methyl qPCR technology."

The EpiTect Methyl qPCR Array System is a fast, reliable technology that profiles the DNA methylation status of a panel of genes. These PCR Arrays can help you discover and verify cancer or developmental biomarkers useful for both basic and applied research. No bisulfite conversion is required, and the challenges of real-time PCR primers design and optimization has already been done for you. EpiTect Methyl qPCR Arrays are ideal for fast, high-throughput methylation analysis. For determining the exact methylation level of individual and consecutive CpG sites, we recommend using bisulfite Pyrosequencing on a PyroMark system.

You can use any 96-well or 384-well real-time PCR instrument.
Click below for detailed information.

How it Works Performance Data Application Data

How it Works

The EpiTect Methyl qPCR Array System relies on the differential cleavage of target sequences by two different restriction endonucleases whose activities require either the presence or absence of methylated cytosines in their respective recognition sequences. As real-time PCR quantifies the relative amount of DNA remaining after each enzyme digestion, the methylation status of individual genes and the methylation profile across a gene panel are reliably and easily calculated. The high yield of DNA from the restriction digests and PCR amplification allow the analysis of smaller, more heterogeneous samples.

Download User Manual  Tour the FREE Data Analysis Template

What It Offers:

  • Guaranteed Performance - Ready-to-use for DNA methylation analysis
  • Time & Cost Savings - Less than 30 min hands-on time to analyze 24 or 96 genes
  • Easy Data Analysis - FREE Excel-based data analysis template available

You can easily perform a DNA Methylation experiment in your own laboratory using any 96-well or 384-well real-time PCR instrument that you have access to.
Or you can send your DNA samples to us and take advantage of our PCR Array Services.

Array Layout:
The PCR Arrays are available in both 96- and 384-well plate formats to analyze the methylation status of 24 or 96 genes related to a disease state, such as specific types of cancer, or development pathways related to specific cells or tissues. The Signature panels of 24 genes are arranged on either 96-well or 384-well plates to simultaneously characterize all four restriction digests from either one or four different DNA samples, respectively. The more Complete panels of 96 genes are arranged on 96- or 384-well plates to characterize all four restriction digests from one DNA sample either on four plates or all on the same plate, respectively.

For more detail on PCR Array layout, see the "Gene Table" link for the individual array products.

Performance Data

To verify the reliability of the EpiTect Methyl qPCR Array System, its results and sensitivity were compared with bisulfite Sanger sequencing, the gold standard in DNA methylation analysis.

Same Results as Sanger Bisulfite Sequencing

EpiTect Methyl qPCR Yields Results Identical to Sanger Bisulfite Sequencing.
The methylation status of the cadherin 1 (CDH1) gene promoter was analyzed using either bisulfite sequencing or EpiTect Methyl qPCR Primer Assays in three different breast cancer cell lines known to have very different CDH1 methylation patterns.

Same Sensitivity as Sanger Bisulfite Sequencing
Primary tumors are typically very heterogeneous, containing a mixture of both cancerous and noncancerous cells. Therefore, reliable tumor characterization requires detecting smaller amounts of hypermethylated DNA diluted in an unmethylated background.

EpiTect Methyl qPCR Detects Hypermethylation in Heterogeneous Samples Containing As Little As Five Percent Tumor DNA.
SKBR3 breast cancer cell line and normal blood genomic DNA (encoding hypermethylated and unmethylated HIC1, respectively) were mixed in different ratios. Using Human HIC1 EpiTect Methyl qPCR Primers, the percentage of hypermethylated HIC1 relative to total promoter DNA in each mixture was detectable even down to five percent of the total DNA sample.

Application Data

Gene promoter methylation is the most common epigenetic mechanism silencing tumor suppressor genes during oncogenesis. Almost all cancer-related signaling pathways are affected by methylation, and the number of genes affected in each major type of cancer is still rapidly growing. However, even the most relevant genes have not yet been correlated to individual cancer types or subtypes in order to better define biological pathways and mechanisms leading to oncogenesis and in order to properly develop DNA methylation biomarkers. The expenses related to screening large numbers of genes in many tumor samples simultaneously using a bisulfite-based method are not practical. The EpiTect Methyl qPCR System provides an ideal reagent for such studies. The following experiments demonstrate that DNA Methylation PCR Arrays can both verify known and discover new DNA methylation cancer biomarkers. For determining exact methylation levels of specific CpG sites, we recommend using bisulfite Pyrosequencing on a PyroMark system.

Biomarker Verification

EpiTect Methyl qPCR Arrays Verify Breast Cancer Gene Methylation Status in Breast Cancer Cell Lines.
The heat map compares the hypermethylation status of 24 genes in the genomic DNA of three breast cancer cell lines and blood genomic DNA (used as an unmethylated control) determined with the Human Breast Cancer Signature Panel DNA Methylation PCR Arrays. The results further strengthen the correlation of these biomarkers with breast cancer.

Biomarker / Pathway Discovery
Cancer progresses through aberrant cell differentiation due to alterations in gene expression. Transcription factors regulate gene expression, and many tumor suppressor genes and oncogenes, defined by classical genetic methods, encode transcription factors. Does the methylation status of transcription factor genes differ between cancer and normal cells?

EpiTect Methyl qPCR Arrays Discover New Candidate Breast Cancer DNA Methylation Biomarkers.
The heat map compares the hypermethylation status of a panel of 79 transcription factor genes in six different breast cancer cell lines (some in duplicate) and a normal epithelial cell line as determined using 384-well Custom DNA Methylation PCR Arrays. These breast cancer cell lines also hypermethylate this gene panel potentially providing a new source of cancer biomarkers.

These results are consistent with the notions that aberrant expression of transcription factors controlling cell differentiation plays key roles in oncogenesis and that transcription factors can be tumor suppressors.


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Functional Gene Grouping How It Works Manual & Resources Reagents & Software
User Manual EpiTect Methyl qPCR Array User Manual  (PDF)
Data Analysis Free PCR Array Data Analysis Software 
Other Needed Materials Accessories, Equipment & Reagents Required for Methylation Analysis
Web Seminars Attend a live on-line seminar hosted by an Applications Scientist about PCR
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Functional Gene Grouping How It Works Manual & Resources Reagents & Software

The complete EpiTect Methyl qPCR Array System insures that you will get good results from your DNA methylation analysis experiment the first time, and every time guaranteed.

The Complete EpiTect Methyl qPCR Array System Includes:

EpiTect Methyl qPCR Arrays
Analyze the DNA Methylation Status of 24 or 96 Genes Simultaneously

EpiTect Methyl DNA Restriction Kit
Required for a complete and successful experiment
Includes enzymes and a digestion buffer optimized for complete digestion by both enzymes under the same conditions

RT² SYBR® Green qPCR Master Mixes
Instrument-specific PCR master mixes insure high-efficiency, sequence-specific amplification

Data Analysis Software (Excel template)

Our convenient and high-quality real-time RT-PCR accessory products complete the EpiTect Methyl qPCR Array System. The other components needed for real-time PCR analyzing profiles of methylation status are a SYBR® Green qPCR master mix matched to the instrument in your laboratory, and the EpiTect Methyl DNA Restriction Kit.

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