DNAm of bisulfite-converted blood DNA samples were analyzed with the Infinium HumanMethylationEPIC BeadChip™ Kit (WG-317-1002, Illumina) as previously described [14 (link)–16 (link), 18 (link)]. The samples were placed on EPIC array chips randomly to avoid potential confounding batch effects. Thus, there were no distortion of sample placement across those chips. DNAm data of 24 CpG sites on the TNF gene, 14 CpG sites on the IL1B gene, and 14 CpG sites on the IL6 gene were extracted and analyzed.
Infinium humanmethylationepic beadchip kit
Manufactured by Illumina
Sourced in United States
The Infinium HumanMethylationEPIC BeadChip Kit is a microarray-based assay designed to analyze the DNA methylation status of over 850,000 CpG sites across the human genome. It provides a comprehensive and efficient way to study DNA methylation patterns at a genome-wide scale.
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Lab products found in correlation
Ez dna methylation kit, by Zymo Research (5 mentions)
Iscan platform, by Illumina (3 mentions)
Qubit dsdna broad range assay kit, by Thermo Fisher Scientific (3 mentions)
Masterpure dna extraction kit, by Illumina (3 mentions)
Epitect fast 96 dna bisulfite kit, by Qiagen (2 mentions)
Masterpure dna purification kit, by Illumina (1 mentions)
Methylationepic beadchip, by Illumina (1 mentions)
Ez 96 dna methylation kit, by Zymo Research (1 mentions)
Genomestudio, by Illumina (1 mentions)
Qubit fluorometer, by Thermo Fisher Scientific (1 mentions)
Beadarray scanner, by Illumina (1 mentions)
Iscan scanner, by Illumina (1 mentions)
12 protocols using infinium humanmethylationepic beadchip kit
1
Genome-wide DNA Methylation Analysis
2
EPIC Array-Based Genome-Wide DNA Methylation Profiling
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DNA was extracted from whole blood following the MasterPure™ DNA Purification kit (Epicentre, MCD 85201). DNA passing quality control based on NanoDrop spectrometry and in sufficient amount through the Qubit dsDNA Broad Range Assay Kit (ThermoFischer Scientific, Q32850) was selected for analysis for genome-wide DNAm status. 500 ng of genomic DNA from each sample was bisulfite-converted with the EZ DNA Methylation™ Kit (Zymo Research, D5002) and analyzed using Infinium HumanMethylationEPICBeadChip™ Kit (Illumina, WG-317-1002). The Illumina iScan platform scanned the arrays.
3
Methylome Analysis of Brain, Blood, Saliva, and Buccal Samples
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Methylome assays were performed as previously described. Briefly, genomic DNA from saliva, buccal, and whole blood were isolated with the MasterPureTM DNA extraction kit (Epicenter, MCD85201). DNA was bisulfite-converted using the EZ DNA Methylation™ Kit (Zymo Research, D5002). The Infinium HumanMethylationEPIC BeadChip™ Kit (Illumina, WG-317-1002) was used to analyze DNAm of 21 subjects with brain, blood, saliva, and buccal samples. Raw data was processed using the R packages RnBeads and Minfi (Aryee et al., 2014 (link); Fortin et al., 2017 (link)); this enables quality control checks, data filtering, and normalization of the data in addition to differential methylation analyses (Aryee et al., 2014 (link); Assenov et al., 2014 (link); Fortin et al., 2017 (link)).
4
Profiling DNA Methylation Landscapes
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DNA from BAL cells was processed using the TrueMethyl conversion kit (Cambridge Epigenetix) workflow in order to investigate true methylation (5mC) by using oxidative bisulphite treatment (oxBS), and total methylation (5mC + 5hmC) by regular common non-oxidative bisulphite treatment (BS). DNA methylome profiling was carried out using the Infinium HumanMethylationEPIC BeadChip Kit (Illumina), which interrogates over 850,000 CpG sites. Methylation arrays were processed by the National Genomics Infrastructure (NGI), Science for Life Laboratory at Uppsala University. Samples were randomised according to smoking-status, age, gender, and cell-proportion and processed together with technical replicates in one run. DNA methylation β-values from the technical replicates correlated strongly with a Pearson correlation value of 0.992 (P = 2.2 × 10–16). Raw intensity IDAT format files were used for subsequent array analysis.
5
Genome-wide DNA Methylation Profiling
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Methylation profiling has been conducted on DNA samples using the Illumina Methylation EPIC BeadChip which integrates over 850,000 Methylation sites across the genome. A five hundred–nanogram samples of whole-blood DNA from 1,175 persons were treated with sodium bisulfite using the EZ96 DNA methylation kit (Zymo Research, Irvine, CA, USA) following the manufacturer’s standard protocol. DNA methylation was assessed using the Illumina Infinium HumanMethylationEPIC BeadChip kit (Illumina, Inc., San Diego, CA, USA) [42 (link)]. Raw signal intensities were pre-processed, normalised, and converted into β values using the Bioconductor bigmelon package [43 (link)].
6
Genome-wide DNA Methylation Analysis
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Genomic DNA was extracted from whole blood tissues with the MasterPure DNA extraction kit (MCD85201, Epicenter, Madison, WI, USA) following the recommended protocol. DNA quality was assessed with NanoDrop spectrometry and quantified with the Qubit dsDNA Broad Range Assay Kit (Q32850, ThermoFisher Scientific, Waltham, MA, USA). For each sample, 500 ng of DNA was bisulfite‐converted with the EZ DNA Methylation Kit (D5002, Zymo Research, Irvine, CA, USA). The Infinium HumanMethylationEPIC BeadChip Kit (WG‐317‐1002, Illumina, San Diego, CA, USA) was used to analyze genome‐wide DNAm. The arrays were scanned with the Illumina iScan platform.
The R packages ChAMP and Minfi were used to process the raw methylation data. During the loading of data, probes were filtered out if they (i) had a detection P‐value >0.01, (ii) had <3 beads in at least 5% of samples per probe, (iii) were non‐CpG, SNP related, or multi‐hit probes, (iv) were located on chromosome X or Y. Samples were normalized with beta‐mixture quantile dilation before performing differential methylation analyses.
The R packages ChAMP and Minfi were used to process the raw methylation data. During the loading of data, probes were filtered out if they (i) had a detection P‐value >0.01, (ii) had <3 beads in at least 5% of samples per probe, (iii) were non‐CpG, SNP related, or multi‐hit probes, (iv) were located on chromosome X or Y. Samples were normalized with beta‐mixture quantile dilation before performing differential methylation analyses.
7
DNA Methylation Analysis via Bisulfite-Treated Samples
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Prior to DNA quantification, DNA samples containing precipitated material were heated to 65°C and centrifuged. Thereafter, 1 μg of DNA was bisulfite-treated using the EpiTect® Fast 96 DNA Bisulfite Kit (Qiagen Hilden, Germany) and analysed using the Infinium Human MethylationEPIC BeadChip Kit (Illumina, CA, USA) according to the manufacturer’s protocol.
8
Genome-Wide DNA Methylation Analysis
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Genomic DNA extraction was performed as described previously [22 (link)]. A 400‐ng aliquot of genomic DNAs was quantified by Qubit Fluorometer (Life Technologies, Carlsbad, CA, USA) and bisulfite‐converted using an EZ DNA Methylation Kit (Zymo Research, Irvine, CA, USA). Methylation array was conducted using the Infinium Human MethylationEPIC BeadChip Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. The raw signal intensity for methylated and unmethylated DNA was measured using a BeadArray Scanner (Illumina). After color‐bias correction, background subtraction of the signal intensities and interarray normalization on Genome Studio (Illumina), the raw methylation value (β‐value) for each CpG was defined as M/(M + U + 100), where M and U were the intensities of methylated and unmethylated probes, respectively. CpG loci located 0–500 bp upstream of transcript start sites (TSS) were used for the analysis of methylation status in promoters.
9
Genome-Wide DNA Methylation Profiling
10
Genome-wide DNA Methylation Analysis
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One microgram of DNA was bisulfite-treated using the EpiTect® Fast 96 DNA Bisulfite Kit (Qiagen Hilden, Germany) and analysed using the Infinium Human Methylation EPIC BeadChip Kit (Illumina, CA, USA) according to the manufacturer’s protocol.
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