Methylation Standards

<h2>What are methylation standards?</h2>
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Methylation standards are defined reference DNA materials with a known and confirmed methylation status, ranging from a fully methylated DNA (where every cytosine at CpG or other sites carries a methyl group) to a fully unmethylated DNA (where no cytosines are methylated) and intermediate or mixed standards containing a defined ratio of the two. The most widely used unmethylated control in bisulfite sequencing is lambda phage DNA, which is naturally unmethylated and can be spiked into a conversion reaction to estimate conversion efficiency.
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<h2 dir="ltr">What you will find:</h2>
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<ul>
<li dir="ltr" role="presentation">Methylated and non-methylated DNA control sets for comparative epigenetic analysis and assay validation</li>
<li dir="ltr" role="presentation">Universal methylated DNA standards for methylation assessment workflows</li>
<li dir="ltr" role="presentation">Genomic DNA reference materials: for microbial and human methylation studies</li>
<li dir="ltr" role="presentation">Matched DNA sets: used in experimental models for controlled comparison of methylation status&nbsp;</li>
<li dir="ltr" role="presentation">Bisulfite-converted DNA standards: for downstream sequencing-based methylation and PCR analysis</li>
<li dir="ltr" role="presentation">Methylation spike-in controls: for sequencing normalization and high-throughput workflows</li>
<li dir="ltr" role="presentation">Mouse and human DNA methylation reference sets: for specific species epigenetic studies</li>
<li dir="ltr" role="presentation">Methylated DNA IP control kits for methylation assays involving immunoprecipitation</li>
</ul>
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<h2>How to use methylation standards</h2>
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Spike an unmethylated control into every bisulfite or enzymatic conversion reaction
Running an unmethylated DNA like lambda phage DNA alongside your samples in the same conversion reaction estimates the conversion efficiency of that specific run, since every remaining cytosine signal after conversion should be treated as a false positive, and this rate can be quantified and accounted for in downstream analysis.
Run a fully methylated positive control to confirm methylated cytosines are preserved
A fully methylated standard, such as DNA synthesized with 5-methyl-dCTP or commercially prepared methylated genomic DNA, confirms your conversion workflow correctly preserves methylated cytosines intact rather than inadvertently converting them, which would produce false-negative methylation calls.
Use a mixed or intermediate standard to calibrate quantitative methylation assays
A standard containing a defined ratio of methylated to unmethylated DNA, or a set of standards spanning a range of methylation percentages, provides a calibration curve for quantitative methylation assays like 5-methylcytosine ELISA, validating that the assay reports the expected methylation level across its full dynamic range.
Confirm standard stability before long-term storage or lot-to-lot use
Methylation control DNA has documented stability windows, and confirming that your standard's methylation status is stable under storage conditions, and consistent across lots, is necessary for reliable longitudinal monitoring of conversion efficiency.
Use standards to monitor workflow consistency over time
Running a conversion control in every batch allows longitudinal tracking of conversion efficiency across instrument runs, reagent lots, and protocol variations, helping catch workflow drift before it affects real sample results.
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<h2>Specifications context</h2>
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Lambda phage DNA is the most commonly used unmethylated bisulfite conversion control because it is naturally unmethylated, commercially available, and well characterized, and it can be aligned to the known lambda phage reference genome after sequencing to calculate residual unconverted cytosine rates, providing a direct, interpretable measure of conversion efficiency. As of 2026, fully methylated and fully unmethylated standard sets are also used alongside enzymatic methyl-seq conversions to confirm that EM-seq's enzymatic mechanism correctly protects methylated cytosines and converts unmethylated ones, independent of the conversion chemistry used.
This category sits within DNA/RNA Methylation, alongside Bisulfite Conversion Kits, Non-Bisulfite Kits &amp; Reagents, and ELISA Kits &amp; Reagents. See the full reagents catalog and use Quick Order for recurring orders.
<a href="https://mbpinc.net/contact-us">Contact the expert team of Molecular Biology Products Inc. (MBP)</a> to get high-quality methylation standards for your lab today.

MSDS

Protocol

Bisulfite Converted Universal Methylated Human DNA Standard

Bisulfite Converted Universal Methylated Human DNA Standard (D5015) by Zymo Research — pre-converted human brain genomic DNA with >95% CpG methylation, 20 ng/µl, 1 µg/50 µl (50 reactions). Includes MLH1 validation primers.

Concentration

Sample Storage

Manufacturer

Shipping Condition

Storage Condition

E. coli Non-Methylated Genomic DNA (5 µg/20 µl)

D5016 by Zymo Research is 5 µg (250 ng/µL, 20 µL) of fully unmethylated E. coli genomic DNA from Dam–/Dcm– strain ER2925, in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0). Used as a negative control or bisulfite conversion efficiency spike-in in WGBS, RRBS, MSP, and epigenetic array workflows. Store at ≤–20°C.

Genotype

Storage

Human Matched DNA Set

The Human Matched DNA Set by Zymo Research is a matched pair of human genomic DNA from brain and spleen of a single individual, precisely quantified by LC/MS for 5-methylcytosine and 5-hydroxymethylcytosine content, for use as a two-point epigenetic control in 5mC and 5hmC detection workflows. Available as complete matched set (D5018), brain DNA only (D5018-1), or spleen DNA only (D5018-2).

Sample Source

Human Brain DNA (5 µg)

Human Spleen DNA (5 µg)

D5013-Data Sheet

D5013 - MSDS

D5013-Protocol

Human Methylated & Non-Methylated (WGA) DNA Set

The Human Methylated & Non-Methylated (WGA) DNA Set by Zymo Research is a human DNA control set comprising whole-genome amplified (WGA) methylated (&gt;95% CpG methylated) and non-methylated DNA from the HCT116 DKO cell line, plus RASSF1 primers, for use as positive and negative controls in bisulfite sequencing, MSP, and methylation array workflows. Available as complete set with primers (D5013), non-methylated DNA only (D5013-1), or methylated DNA only (D5013-2).

Human Methylated & Non-Methylated (WGA) DNA Set (DNA w/ Primers)

Human WGA Non-Methylated DNA (5 µg/20 µl)

Human WGA Methylated DNA (5 µg/20 µl)

D5014-Data  Sheet

D5014 - MSDS

D5014-Protocol

Human Methylated & Non-methylated DNA Set

Zymo Research Human Methylated &amp; Non-methylated DNA Set: HCT116 DKO-derived 250 ng/µl genomic DNA standards with DAPK1 primers. Complete set (D5014), non-methylated only (D5014-1, &lt;5% CpG), or methylated only (D5014-2, &gt;95% CpG). 5 µg/20 µl each. Store ≤−20°C.

Format

Human Methylated & Non-methylated DNA Set (DNA w/ Primers)

Human HCT116 DKO Non-Methylated DNA (5 µg/20 µl)

Human HCT116 DKO Methylated DNA (5 µg/20 µl)

Methylated & Non-methylated pUC19 DNA Set

D5017 by Zymo Research provides paired methylated and non-methylated pUC19 plasmid DNAs (1 ng/µl each, linearized by ScaI) plus pUC19MN primers for monitoring bisulfite conversion efficiency and calibrating DNA methylation quantitation assays. The methylated variant is fully CpG-methylated via CpG Methylase; the non-methylated variant is propagated in a Dam⁻/Dcm⁻ strain, ensuring no residual Dam or Dcm methylation. Suitable for WGBS spike-in, targeted bisulfite sequencing QC, and methylation standard curve construction.

Additional Info

Methylated-DNA IP Kit (10 Rxns.)

The D5101 by Zymo Research is a 10-reaction Methylated-DNA IP Kit for immunoprecipitation of 5mC-containing DNA from 50–500 ng fragmented genomic input, achieving &gt;100-fold methylated DNA enrichment using Anti-5-Methylcytosine Monoclonal Antibody Clone 7D21. The full workflow completes in approximately 4 hours and eluted DNA is compatible with MeDIP-seq, bisulfite sequencing, PCR, and microarray analysis.

Applicable For

Elution Volume

Input

Processing Time

Methylated/Non-methylated Control DNA & Primer Set

D5101-2 by Zymo Research is the Methylated/Non-methylated Control DNA &amp; Primer Set — 1:4 methylated:non-methylated pUC19 mixture at 1 ng/µL total (250 pg/µL pUC19m + 750 pg/µL pUC19) with control primers yielding a 350 bp amplicon. Used as a MeDIP enrichment QC spike-in; successful IP shifts the ratio to ≥10:1. NcoI digestion differentiates pUC19m from pUC19 post-PCR. Store at –20°C.

Mouse 5-hmC & 5-mC DNA Set

Mouse 5-hmC & 5-mC DNA Set (D5019) by Zymo Research — four organ-specific genomic DNAs (brain, kidney, liver, thymus) at 250 ng/µl, 5 µg per organ, with LC/MS-verified 5-hmC and 5-mC levels for epigenetic assay validation. Available as the full set (D5019) or individual tissue DNAs (D5019-1 through D5019-4).

Mouse Brain DNA (5 µg)

Mouse Kidney DNA (5 µg)

Mouse Liver DNA (5 µg)

Mouse Thymus DNA (5 µg)

DataSheet

D5011 - MSDS

D5012 - MSDS

D5011-Protocol

D5012-Protocol

Universal Methylated DNA Standard

Zymo Research Universal Methylated DNA Standards: 250 ng/µl genomic DNA with &gt;95% CpG methylation (M.SssI) + bisulfite PCR primer set. Human (D5011, male brain) and Mouse (D5012). Positive control for bisulfite conversion and methylation assays. Store ≤−20°C.

Universal Methylated Human DNA Standard

Universal Methylated Mouse DNA Standard

Zymo-Seq Methyl Spike-in Control

D5500 by Zymo Research is the Zymo-Seq Methyl Spike-in Control, containing six synthetic amplicons (180–200 bp) at 0%, 10%, 25%, 50%, 75%, and 100% cytosine methylation for monitoring bisulfite conversion efficiency in WGBS and RRBS workflows. Provides 25 preparations at 60 pg/µl; store at -20°C. Research use only.