DNA was extracted from the sorted cells by using a DNA-extraction kit (QIAGEN) and then bisulfite treated using an EZ DNA methylation kit (Zymo Research). The bisulfite-modified DNA-sequencing library was generated using the EpiGnome™ kit (Epicenter) per the manufacturer’s instructions. WGBS was performed as described previously. Briefly, bisulfite-modified DNA sequencing libraries were generated using the EpiGenome kit (Epicenter) according to the manufacturer’s instructions. Bisulfite-modified DNA libraries were sequenced using Illumina HiSeq 4000 and NovaSeq 6000 systems (Abdelsamed et al., 2017 (link)). Sequencing data were aligned to the HG19 genome using the BSMAP v. 2.74 software (Xi and Li, 2009 (link)). Differential analysis of CpG methylation among the datasets was determined with a Bayesian hierarchical model to detect regional methylation differences with at least three CpG sites (Wu et al., 2015 (link)). Data are shown from only samples that yielded enough genomic material (~or > 2,000 cells) for genome-wide sequencing coverage and other quality control parameters. Notably, bisulfite modification for the patient 15 week 2 sample had low conversion (deamination of unmethylated cytosines) and was therefore excluded from methylation analyses.
Epigenome kit
Manufactured by Illumina
The EpiGenome kit is a laboratory equipment product offered by Illumina. It is designed to facilitate the analysis of epigenomic data. The core function of the EpiGenome kit is to enable the processing and analysis of DNA samples to study epigenetic modifications and their impact on gene expression and cellular function.
Automatically generated - may contain errors
2 protocols using epigenome kit
1
Whole-Genome Bisulfite Sequencing of Sorted Cells
2
Whole-Genome Bisulfite Sequencing of Sorted Cells
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DNA was extracted from the sorted cells by using a DNA-extraction kit (QIAGEN) and then bisulfite treated using an EZ DNA methylation kit (Zymo Research). The bisulfite-modified DNA-sequencing library was generated using the EpiGnome™ kit (Epicenter) per the manufacturer’s instructions. WGBS was performed as described previously. Briefly, bisulfite-modified DNA sequencing libraries were generated using the EpiGenome kit (Epicenter) according to the manufacturer’s instructions. Bisulfite-modified DNA libraries were sequenced using Illumina HiSeq 4000 and NovaSeq 6000 systems (Abdelsamed et al., 2017 (link)). Sequencing data were aligned to the HG19 genome using the BSMAP v. 2.74 software (Xi and Li, 2009 (link)). Differential analysis of CpG methylation among the datasets was determined with a Bayesian hierarchical model to detect regional methylation differences with at least three CpG sites (Wu et al., 2015 (link)). Data are shown from only samples that yielded enough genomic material (~or > 2,000 cells) for genome-wide sequencing coverage and other quality control parameters. Notably, bisulfite modification for the patient 15 week 2 sample had low conversion (deamination of unmethylated cytosines) and was therefore excluded from methylation analyses.
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