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Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing

ABSTRACT: Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing

PROVIDER: PRJNA528654 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9888310_1.fastq.gz	Fastqsanger.gz
	SRR9888310_2.fastq.gz	Fastqsanger.gz
	SRR9888320_1.fastq.gz	Fastqsanger.gz
	SRR9888320_2.fastq.gz	Fastqsanger.gz
	SRR9888330_1.fastq.gz	Fastqsanger.gz

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Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing [Beadchip]

Project description:We systematically evaluated alternate strategies for WGBS studies, taking into account opportunites around library preparation methods, sequencing platforms and analysis pipeline optimization. We also assessed the performance and precision of the WGBS method relative to the methylation arrays, in an effort to provide data-driven recommendations for future WGBS studies, in particularly with respect to minimum coverage.

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Project description:Whole genome bisulfite sequencing (WGBS), with its ability to interrogate methylation status at single CpG site resolution epigenome-wide, is a powerful technique for use in molecular experiments. Here, we aim to advance strategies for accurate and efficient WGBS for application in future large-scale epidemiological studies. We systematically compared the performance of three WGBS library preparation methods with low DNA input requirement (Swift Biosciences Accel-NGS, Illumina TruSeq and QIAGEN QIAseq) on two state-of-the-art sequencing platforms (Illumina NovaSeq and HiSeq X), and also assessed concordance between data generated by WGBS and methylation arrays. Swift achieved the highest proportion of CpG sites assayed and effective coverage at 26x (P < 0.001). TruSeq suffered from the highest proportion of PCR duplicates, while QIAseq failed to deliver across all quality metrics. There was little difference in performance between NovaSeq and HiSeq X, with the exception of higher read duplication rate on the NovaSeq (P < 0.05), likely attributable to the higher cluster densities on its flow cells. Systematic biases exist between WGBS and methylation arrays, with lower precision observed for WGBS across the range of depths investigated. To achieve a level of precision broadly comparable to the methylation array, a minimum coverage of 100x is recommended.

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Project description:This SuperSeries is composed of the SubSeries listed below.

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