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Whole Genome Bisulfite Sequencing

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whole genome bisulfite sequencing By Christoph Bock (Max Planck Institute for Informatics) (Own work) [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons
DNA methylation at the C5 position of cytosine plays a crucial role in gene expression and chromatin remodeling. Perturbations in methylation patterns are implicated in the development of cancer, neurodegenerative diseases and neurological disorders. Therefore, the deep reach of the methylome is vital to understanding gene expression and other processes that are subject to epigenetic regulation. Novogene provides whole genome sequencing of bisulfite-converted DNA as an effective method to identify individually methylated cytosines on a genome-wide scale. Methylome analysis is an increasingly valuable research tool with a range of applications, including studies on gene regulation, cell differentiation, embryogenesis, aging, tumorigenesis, phenotypic diversity and evolution in plants and animals.

The Novogene Advantage

  • Extensive experience: Over 500 projects successfully completed by a bioinformatics analysis team composedof Ph.D. scientists entirely.
  • Unsurpassed data quality: We guarantee that ≥ 80% of bases have a sequencing quality score ≥ Q30, exceeding Illumina’s official guarantee of ≥ 75%.
  • Comprehensive data analysis: We use widely-accepted mainstream software such as Bismark and a mature in-house pipeline for mapping, Differentially Methylated Region (DMR) analysis, functional analysis and data visualization.

Project Workflow

whole genome bisulfite sequencing project workflow

Sequencing Strategy

  • 200-400-bp insert bisulfite treat DNA library
  • NovaSeq6000 platform, paired-end 150 bp

Data Quality Guarantee

  • Over 80% of bases have a sequencing quality score ≥ Q30. See examples of our high quality data.

Sample Requirements

  • DNA amount: ≥ 3.0 μg
  • DNA concentration: ≥ 20 ng/μl
  • DNA volume: ≥ 20 μl
  • Purity: OD260/280 = 1.8–2.0 without degradation,no protein or RNA contamination

Turnaround Time

  • 25 working days from verification of sample quality without data analysis
  • The data analysis turnaround is project-dependent

Recommended Sequencing Depth

  • Sequencing depth ≥30× coverage

Analysis Pipeline

WGBS Analysis Pipeline

whole genome biosulfite sequencing analysis pipeline
Table. Representative samples showing data quality of Novogene’s whole genome bisulfite sequencing service.
Sample Name Raw Reads Raw Bases Clean Reads Clean Bases Error Rate (%) Q20 (%) Q30 (%) GC (%) bisulfite Conversion Rate (%)
Sample 1 750864918 112.63 G 686418034 102.96 G 0.03 94.62 86.52 23.01 99.29
Sample 2 762188782 114.14 G 618495260 92.61 G 0.04 94.35 86.41 21.08 99.66
Sample 3 789026912 118.35 G 721080112 108.16 G 0.02 96.54 90.63 21.12 99.66
Sample 4 784535120 117.68 G 760489944 114.07 G 0.03 92.81 85.49 20.70 99.63

Project Example

The following study utilized Novogene's WGBS and RNA-Seq services. Lineage-specific functions of TET1 in the postimplantation mouse embryo Nature Genetics, 49 (7): 1061-1072 (2017) The TET enzymes are essential epigenetic regulators and also play a significant role in embryo implantation. Novogene’s whole genome bisulfite sequencing (WGBS) service, together with RNA sequencing, was adopted to explore the non-redundant functions of one TET enzyme, TET1, in the post-implantation mouse embryo. TET1 enzyme was shown to regulate lineage-specific genes in the pre-streak mouse epiblast and suppress metabolic genes in the extraembryonic ectoderm. TET1 was also found to be involved in the DNA methylome regulation of epiblast-like cells. While loss of TET1 affected the EpiLC methylome, the gene expression of more than 90% of associated genes was not affected. Further studies demonstrated the catalytic activity of telomere maintenance, via the ZSCAN4 locus, and the catalytic-independent repression of target genes. The interplay between catalytic and non-catalytic activities in TET1 was regulated through the transcriptional repressor, JMJD8. This study highlights how the complex interplay and functions of TET1 in normal embryo development were identified using WGBS as a tool.
wgbs-data Figure. Heat map cluster of the differentially expressed genes that are regulated by TET1 in the epiblast

Publications Using Novogene’s Expertise

Journal Title
Nature Communications, 3:850 (2012) An atlas of DNA methylomes in porcine adipose and muscle tissues.
Genome Biology, 15: R49 (2014) Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain.
Bioinformatics, 33(11):1591-1595 (2017) Genome-wide analysis of DNA methylation profiles in a senescence-accelerated mouse prone 8 brain using whole-genome bisulfite sequencing.
Nature Genetics, 49(7):1061-1072 (2017) Lineage-specific functions of TET1 in the postimplantation mouse embryo.