Ez 96 dna methylation magprep kit

Manufactured by Zymo Research

Sourced in United States

The EZ-96 DNA Methylation MagPrep Kit is a laboratory equipment product designed for the purification and bisulfite conversion of DNA samples. It utilizes magnetic bead technology to facilitate efficient DNA extraction and preparation for methylation analysis.

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Lab products found in correlation

Infinium methylationepic beadchip, by Illumina (3 mentions) Hybridization oven, by Illumina (2 mentions) Iscan microarray scanner, by Illumina (2 mentions) Freedom evo robot, by Tecan (2 mentions) Infinium humanmethylation450 beadchip, by Illumina (2 mentions) M elution buffer, by Zymo Research (2 mentions) Epic methylation array, by Illumina (2 mentions) Qubit dsdna br assay kit, by Thermo Fisher Scientific (2 mentions) Beadchips, by Illumina (1 mentions) Quant it picogreen dsdna quantitation, by Thermo Fisher Scientific (1 mentions) Clotspin basket, by Qiagen (1 mentions) Kingfisher flex robot, by Thermo Fisher Scientific (1 mentions)

9 protocols using ez 96 dna methylation magprep kit

Genome-Wide DNA Methylation Profiling

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Isolated DNA was bisulfite converted using the EZ-96 DNA Methylation MagPrep Kit (Zymo Research). Converted DNA was applied to either an Illumina Infinium HumanMethylation450 BeadChip (450K) or an Infinium MethylationEPIC BeadChip Kit (EPIC) according to the manufacturers’ protocol to measure methylation at ∼450,000 (450K) or 850,000 (EPIC) CpG sites genome wide.

Martos S.N., Campbell M.R., Lozoya O.A., Wang X., Bennett B.D., Thompson I.J., Wan M., Pittman G.S, & Bell D.A. (2020). Single-Cell Analyses Identify Dysfunctional CD16+ CD8 T Cells in Smokers. Cell Reports Medicine, 1(4), 100054.

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DNA Methylation Analysis Using Infinium HumanMethylation450 Assays

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Genomic DNA was bisulfite-converted using an EZ-96 DNA Methylation MagPrep Kit (Zymo Research) according to the manufacturer’s instructions. We applied 500 ng or 250 ng of genomic DNA to bisulfite treatment, and eluted purified, bisulfite-converted DNA in 20 μL or 11 μL of M-Elution Buffer (Zymo Research), respectively. DNA methylation levels were measured using Infinium HumanMethylation450 assays (Illumina) following the manufacturer’s protocol. In brief, 4 μL of bisulfite-converted DNA was isothermally amplified, enzymatically fragmented, and precipitated. Next, precipitated DNA was resuspended in hybridization buffer and dispensed onto Infinium HumanMethylation450 BeadChips (Illumina). To limit batch effects, samples were randomly distributed across slides and arrays. The hybridization was performed at 48 °C for 20 h using a Hybridization Oven (Illumina). After hybridization, BeadChips were washed and processed through a single-nucleotide extension followed by immunohistochemistry staining using a Freedom EVO Robot (Tecan). Finally, the BeadChips were imaged using an iScan Microarray Scanner (Illumina).

Paul D.S., Jones A., Sellar R.S., Mayor N.P., Feber A., Webster A.P., Afonso N., Sergeant R., Szydlo R.M., Apperley J.F., Widschwendter M., Mackinnon S., Marsh S.G., Madrigal J.A., Rakyan V.K., Peggs K.S, & Beck S. (2015). A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation. Genome Medicine, 7, 128.

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High-throughput DNA Methylation Analysis

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A concentration of 400 ng of sample DNA, according to Quant-iTPicoGreen dsDNA quantitation (Life Technologies, Grand Island, NY), was treated with sodium bisulfite using the EZ-96 DNA Methylation MagPrep Kit (Zymo Research, Irvine, CA) according to manufacturer-provided protocol. Bisulfite conversion modifies non-methylated cytosines into uracil, leaving 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) unchanged. High-throughput epigenome-wide methylation analysis, using Infinium MethylationEPICBeadChip (Illumina Inc., San Diego, CA) which uses both Infinium I and II assay chemistry technologies was performed according to manufacturer-provided protocol at CGR. More details are included in the Supplementary Method.

Zhu B., Poeta M.L., Costantini M., Zhang T., Shi J., Sentinelli S., Zhao W., Pompeo V., Cardelli M., Alexandrov B.S., Otlu B., Hua X., Jones K., Brodie S., Dabrowska M.E., Toro J.R., Yeager M., Wang M., Hicks B., Alexandrov L.B., Brown K.M., Wedge D.C., Chanock S., Fazio V.M., Gallucci M, & Landi M.T. (2020). The genomic and epigenomic evolutionary history of papillary renal cell carcinomas. Nature Communications, 11, 3096.

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Genome-wide DNA methylation profiling

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Genomic DNA was bisulfite-converted using an EZ-96 DNA Methylation MagPrep Kit (Zymo Research) according to the manufacturer's instructions. We applied 500 ng of genomic DNA to bisulfite treatment, and eluted purified, bisulfite-converted DNA in 20 μl of M-Elution Buffer (Zymo Research). DNA methylation levels were measured on Infinium HumanMethylation450 BeadChips (Illumina) following the manufacturer's protocol. In brief, 4 μl of bisulfite-converted DNA was isothermally amplified, enzymatically fragmented and precipitated. Next, precipitated DNA was resuspended in hybridization buffer and dispensed onto the BeadChips. To limit batch effects, samples were randomly distributed across slides and arrays. The hybridization was performed at 48 °C for 20 h using a Hybridization Oven (Illumina). After hybridization, BeadChips were washed and processed through a single-nucleotide extension followed by immunohistochemistry staining using a Freedom EVO robot (Tecan). Finally, the BeadChips were imaged using an iScan Microarray Scanner (Illumina).

Paul D.S., Teschendorff A.E., Dang M.A., Lowe R., Hawa M.I., Ecker S., Beyan H., Cunningham S., Fouts A.R., Ramelius A., Burden F., Farrow S., Rowlston S., Rehnstrom K., Frontini M., Downes K., Busche S., Cheung W.A., Ge B., Simon M.M., Bujold D., Kwan T., Bourque G., Datta A., Lowy E., Clarke L., Flicek P., Libertini E., Heath S., Gut M., Gut I.G., Ouwehand W.H., Pastinen T., Soranzo N., Hofer S.E., Karges B., Meissner T., Boehm B.O., Cilio C., Elding Larsson H., Lernmark Å., Steck A.K., Rakyan V.K., Beck S, & Leslie R.D. (2016). Increased DNA methylation variability in type 1 diabetes across three immune effector cell types. Nature Communications, 7, 13555.

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DNA Extraction and Methylation Profiling

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For ACHS-I, DNA was extracted from stored blood clot samples using the PureGene (QIAGEN, 158,389) protocol and Clotspin Baskets (QIAGEN, 158,932). For ACHS-II, whole blood samples (300 µL per extraction) were aliquoted into deep well 96-well plates and genomic DNA was isolated using the Agencourt Genfind v2 Solid Phase Reversible Immobilization (SPRI) paramagnetic bead-based technology (Beckman Coulter, A41497). Prior to bisulphite-conversion, we measured DNA concentrations using a QUBIT dsDNA BR assay kit (Invitrogen, Q32850). The National Cancer Institute’s Cancer Genomics Research Laboratory performed DNA bisulphite conversion using the EZ-96 DNA Methylation MagPrep kit (Zymo Research, D5040) and then ran the bisulphite-converted DNA on Illumina EPIC methylation arrays (Illumina, WG-317-1001).

Pittman G.S., Wang X., Campbell M.R., Coulter S.J., Olson J.R., Pavuk M., Birnbaum L.S, & Bell D.A. (2019). Polychlorinated biphenyl exposure and DNA methylation in the Anniston Community Health Survey. Epigenetics, 15(4), 337-357.

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Epigenome-wide DNA methylation analysis

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Epigenome‐wide DNA methylation was measured using the Infinium MethylationEPIC BeadChip (Illumina Inc., San Diego, CA) following the manufacturer's protocol. Briefly, 500 ng of genomic DNA was bisulfite‐converted using the EZ‐96 DNA Methylation MagPrep Kit (Zymo Research, Irvine, CA, USA) with the KingFisher Flex robot (Thermo Fisher Scientific, Breda, Netherlands). The samples were plated in a randomized order. Bisulfite conversion was performed according to the manufacturer's protocol with the following modifications: 15 μL MagBinding Beads were used for DNA binding, and the conversion reagent incubation was carried out in a cycle protocol of 16 cycles at 95°C for 30 s followed by 50°C for 1 h. After the cycle protocol, the DNA was incubated for 10 min at 4°C. Next, DNA samples were hybridized on the Infinium MethylationEPIC BeadChip (Illumina Inc., San Diego, CA) using 8 μL of bisulfite‐treated DNA as the starting material.

Torma F., Kerepesi C., Jókai M., Babszki G., Koltai E., Ligeti B., Kalcsevszki R., McGreevy K.M., Horvath S, & Radák Z. (2024). Alterations of the gut microbiome are associated with epigenetic age acceleration and physical fitness. Aging Cell, 23(4), e14101.

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Genome-wide Methylation Analysis Using EPIC

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High-throughput genome-wide methylation analysis was performed on bisulfite-treated DNA (EZ-96 DNA Methylation MagPrep Kit (Zymo Research)) at the Cancer Genomics Research Laboratory (CGR) of the National Cancer Institute using the Infinium MethylationEPIC BeadChip (Illumina Inc.) 18 .

Morton L.M., Lee O.W., Karyadi D.M., Bogdanova T.I., Stewart C., Hartley S.W., Breeze C.E., Schonfeld S.J., Cahoon E.K., Drozdovitch V., Masiuk S., Chepurny M., Zurnadzhy L.Y., Dai J., Krznaric M., Yeager M., Hutchinson A., Hicks B.D., Dagnall C.L., Steinberg M.K., Jones K., Jain K., Jordan B., Machiela M.J., Dawson E.T., Vij V., Gastier-Foster J.M., Bowen J., Mabuchi K., Hatch M., Berrington de Gonzalez A., Getz G., Tronko M.D., Thomas G.A, & Chanock S.J. (2024). Genomic characterization of cervical lymph node metastases in papillary thyroid carcinoma following the Chornobyl accident. Nature communications, 15(1).

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Genome-wide DNA Methylation Profiling

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Isolated DNA was bisulfite converted using the EZ-96 DNA Methylation MagPrep Kit (Zymo Research). Converted DNA was applied to either an Illumina Infinium HumanMethylation450 BeadChip (450K) or an Infinium MethylationEPIC BeadChip Kit (EPIC) according to the manufacturers’ protocol to measure methylation at ~450,000 (450K) or 850,000 (EPIC) CpG sites genome wide.

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Automated Extraction of Genomic DNA

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We isolated genomic DNA from whole blood samples (300 μL per extraction) robotically using the Agencourt Genfind v2 Solid Phase Reversible Immobilization (SPRI) paramagnetic bead-based technology (Beckman Coulter). Prior to bisulfite-conversion, DNA concentrations were measured using a QUBIT dsDNA BR assay kit (Invitrogen). The National Cancer Institute’s Cancer Genomics Research Laboratory performed DNA bisulfite conversion using the EZ-96 DNA Methylation MagPrep kit (Zymo Research). Samples were then run on Illumina EPIC methylation arrays (Illumina).

Pittman G.S., Wang X., Campbell M.R., Coulter S.J., Olson J.R., Pavuk M., Birnbaum L.S, & Bell D.A. (2020). Dioxin-like compound exposures and DNA methylation in the Anniston Community Health Survey Phase II. The Science of the total environment, 742, 140424.

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