A QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) was employed in order to extract genomic DNA, which was later treated with RNase A. The quality of the extracted DNA was determined using agarose gel electrophoresisand the BioTekPowerWave XS2 Spectrophotometer (BioTek Instruments, Inc., Winuski, VT, USA). DNA samples that passed quality control were shipped on dry ice to the Australian Genome Research Facility (AGRF), where their quality and quantity were reassessed using the QuantiFluor® dsDNA System (Promega, Madison, WI, USA) and 0.8% agarose gel electrophoresis. After normalization to around 500 ng of DNA per 45 μL, the DNA samples were bisulfite converted using the Zymo EZ DNA Methylation kit (Zymo Research, Owen, CA, USA). Genome-wide methylation profiling was performed on the Infinium MethylationEPICBeadChip microarray (Illumina, San Diego, CA, USA), the latter of which analyzes the methylation patterns of over 850,000 CpG sites.
Infinium methylationepic beadchip microarray
Manufactured by Illumina
Sourced in United States
The Infinium MethylationEPIC BeadChip microarray is a lab equipment product by Illumina. It is designed to analyze DNA methylation across the human genome, covering over 850,000 methylation sites.
Automatically generated - may contain errors
Lab products found in correlation
Zymo ez dna methylation kit, by Zymo Research (5 mentions)
Quantifluor dsdna system, by Promega (4 mentions)
Qiaamp dna mini kit, by Qiagen (3 mentions)
Iscan system, by Illumina (3 mentions)
Biotek powerwave xs2 spectrophotometer, by Agilent Technologies (2 mentions)
450k chip, by Illumina (2 mentions)
Ez dna methylation kit, by Zymo Research (2 mentions)
Powerwave xs2 spectrophotometer, by Agilent Technologies (1 mentions)
Ez dna methylationtm kit, by Zymo Research (1 mentions)
Dneasy blood and tissue kit, by Qiagen (1 mentions)
Allprep dna rna mini kit, by Qiagen (1 mentions)
Nanodrop 8000, by Thermo Fisher Scientific (1 mentions)
Ez 96 dna methylation lightning kit, by Zymo Research (1 mentions)
Ht 12 v4 expression beadchip microarrays, by Illumina (1 mentions)
Iscan device, by Illumina (1 mentions)
Qiasymphony dsp dna kit, by Qiagen (1 mentions)
Genomestudio software, by Illumina (1 mentions)
21 protocols using infinium methylationepic beadchip microarray
1
Genome-wide DNA Methylation Profiling
2
DNA Methylation Profiling in Blood Samples
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DNA methylation levels from whole blood samples were assessed using an Infinium MethylationEPIC BeadChip microarray (Illumina Inc., San Diego, California) according to the manufacturer’s protocol. The wateRmelon package in R was used to process the raw data. After cross-reactive probes and probes that failed quality assessment were removed, a scale-based correction was applied for Illumina type I relative to type II probes. We used a quantile normalization approach to make methylated and unmethylated intensity values identical and then quantified the β-value using the ratio of intensities between methylated and unmethylated alleles [21 (link)]. The residuals of a linear model of β-values as a function of sodium bisulfite modification batch were taken to adjust the values. Measures of blood cells counting for 6 cell types (granulocytes, monocytes, natural killer cells, B cells, CD4+ T cells, and CD8+ T cells) were obtained based on the Houseman estimation method [22 ]. The dataset consisted of β-values for 835 928 CpG sites in 532 individuals.
3
Genome-wide DNA Methylation Profiling
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DNA methylation data from whole blood samples were assessed using an Infinium MethylationEPIC BeadChip microarray (Illumina Inc., San Diego, California) according to the manufacturer’s protocol for the discovery, first, and second replication cohorts (NIAAA and GS). The third replication sample (GTP) and neural tissues from both postmortem cohorts were assessed with the Illumina 450K chip as described previously [37 (link), 38 (link)]. Pre-processing of the GS data has been described in detail elsewhere [39 (link)].
4
DNA Extraction and Methylation Analysis
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A QIAamp DNA Mini Kit (Qiagen, Germany) was used to perform DNA extraction, and optional RNase A digestion was incorporated. DNA purity and integrity were determined by means of the BioTek PowerWave XS2 Spectrophotometer (BioTek Instruments, Inc., USA) and agarose gel electrophoresis, respectively. Genomic DNA that fulfilled our standards for quality and quantity were shipped on dry ice to the Australian Genome Research Facility (AGRF) in Melbourne, where the quality was further ascertained by the QuantiFluor® dsDNA System (Promega, USA). The Zymo EZ DNA Methylation Kit (Zymo Research, USA) was utilized in order to perform bisulfite conversion on the 24 samples. Lastly, the samples were inputted into the Infinium MethylationEPIC BeadChip microarray (Illumina, USA) for a genome-wide interrogation of over 850,000 CpG sites.
5
Genome-wide DNA Methylation Profiling
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Following bisulfite treatment, the DNA methylation status of case and control subjects was assayed using the recently developed Infinium MethylationEPIC BeadChip microarray from Illumina, Inc. (San Diego, CA, USA) according to the manufacturer's instructions, which measured the methylation status of 853,307 CpG sites distributed over the whole genome. The image intensities were extracted using the Illumina iScan system (Illumina, Inc.) and quality-controlled using RnBeads (version 3.5) (18 (link)) in R (www.r-project.org/ ).
6
Infinium MethylationEPIC BeadChip Analysis
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At the AGRF, samples were subject to further quality control measures through assessment on the QuantiFluor® dsDNA System (Promega, Gorman, NC, USA) and via 0.8% agarose gel electrophoresis. The 24 samples were then individually made up to approximately 500 ng of DNA in 45 μL, after which they were bisulfite converted by the Zymo EZ DNA Methylation kit (Zymo Research, Irvine, CA, USA). Finally, the samples were individually inputted into the Infinium MethylationEPIC BeadChip microarray (Illumina, San Diego, CA, USA) for interrogation of over 850,000 CpG sites.
7
Genome-Wide DNA Methylation Analysis
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Genomic DNA was extracted by means of a QIAamp DNA Mini Kit (Qiagen, Hilden, Germany), and optional RNase A digestion was performed. The BioTek PowerWave XS2 Spectrophotometer (BioTek Instruments, Inc., Winuski, VT, USA) was employed in order to determine DNA purity, while agarose gel electrophoresis was carried out in order to examine DNA integrity. For the wart samples only, a second and heavier band was exhibited, pointing towards the presence of the circular dsDNA of HPV. Samples that met the standards for purity and integrity were then shipped on dry ice to the Melbourne node of the Australian Genome Research Facility (AGRF). At the AGRF, the quality of the samples was assessed by the QuantiFluor® dsDNA System (Promega, Madison, WI, USA) and resolution was evaluated via 0.8% agarose gel electrophoresis. The 24 samples were then normalized to approximately 500 ng of DNA in 45 μL and bisulfite converted with Zymo EZ DNA Methylation kit (Zymo Research, Owen, CA, USA). Afterwards, the Infinium MethylationEPIC BeadChip microarray (Illumina, San Diego, CA, USA) was used to carry out a genome-wide analysis of the methylation patterns of over 850,000 CpG sites.
8
Genome-wide DNA Methylation Analysis
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Estimation of DNA methylation profile was performed in a set of 73 EOC patients. At first, bisulfite conversion of 500 ng DNA was done using EZ DNA MethylationTM Kit (Zymo Research, Irvine, CA, USA) according to the manufacturer´s manual. Estimation of genome-wide DNA methylation level for more than 850,000 methylation sites across the genome were done by Infinium MethylationEPIC BeadChip microarray (Illumina Inc.) according to the manufacturer´s recommendations. Microarray was scanned by iSCAN System (Illumina Inc.).
9
DNA Methylation Profiling Using Illumina EPIC
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Participants had a whole blood sample drawn at study entry. The DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) was used to extract DNA from this sample. Unmethylated cytosine residues present in the DNA extract were converted to uracil using the EZ DNA Methylation Kit (Zymo, Irvine, California, USA). DNA methylation profiles were obtained using the Illumina Infinium MethylationEPIC BeadChip microarray which interrogates 863 904 CpG sites and covers 95% of all genes and 95% of CpG islands.16 (link) The ratio of the methylated probe intensity to the overall intensity (β value) was calculated for each CpG and ranged from 0 (all unmethylated) to 1 (all methylated) and then transformed to M-values (log2 ratio of the intensity of the methylated probe to unmethylated CpG probe). CpG probes were filtered based on the detection quality and probes with a detection p>1e−10 were excluded from downstream analyses. In addition, non-CpG, XY-linked, single nucleotide polymorphism (SNP) and cross-hybridisation probes were also removed (839 418 CpGs were retained). Lastly, background correction, normalisation and batch correction were performed using the normal–exponential out-of-band,17 (link) mixture quantile normalisation18 (link) and ComBat19 (link) methods, respectively.
10
DNA Methylation Profiling Across Cohorts
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