Bisulfite Sequencing
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As the first discovered mark, DNA methylation plays a vital role in genome dynamics.
Bisulfite Sequencing is the gold standard for DNA methylation analysis. Coupled with next-generation sequencing technology, it allows for an unbiased genome-wide analysis of DNA methylation and various analyses can be performed on the altered sequence. Combining bisulfite treatment and high-throughput sequencing generates high-accuracy methylome, providing reference for differential DNA methylation analysis across large-scale samples.

Benefits:

  1. Single-base resolution: Analyze methylation state of every Cytosine accurately
  2. Wide applications: Suitable for all the species with accurate genome map

Single Base-Resolution Methylome of the Silkworm Reveals a Sparse Epigenomic Map. Nature Biotechnology 2010. 28:516-520.

Worms

Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis1 and human2, demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.

The DNA Methylome of Human Peripheral Blood Mononuclear Cells.
PloS Biology 2010. 8 (11)

Redcells

Using whole-genome bisulfite sequencing at 24.7-fold coverage, we report a comprehensive (92.62%) methylome and analysis of the unique sequences in human peripheral blood mononuclear cells (PBMC) from the same Asian individual whose genome was deciphered in the YH project. Analysis of the PBMC methylome revealed a rich epigenomic landscape for 20 distinct genomic features, including regulatory, protein-coding, non-coding, RNA-coding, and repeat sequences. Integration of our methylome data with the YH genome sequence enabled a first comprehensive assessment of allele-specific methylation (ASM) between the two haploid methylomes of any individual and allowed the identification of 599 haploid differentially methylated regions (hDMRs) covering 287 genes.

Workflow:

Bioinformatics:

Standard Bioinformatics Analysis

  1. Data Filtering (removing adaptor sequences, contaimination and low-quality reads from raw reads) and Production Statistics
  2. Reads Alignment
  3. Sequence Depth and Coverage Analysis
  4. Calculation of Methylation Level
  5. Global Trends of Methylome
  6. Genome-wide Methylation Profiling
  7. Identification of Differentially Methylated Regions (DMRs)

Custom Bioinformatics Analysis

  1. We can also perform customized analysis to meet requirements of specific projects.

Sample Requirements:

For the genomic DNA samples you will provide:

  1. Purity: OD 260/280=1.8-2.0, without DNA degradation and protein pollution
  2. DNA amount: single library preparation starts from at least 5μg

Recommended Data Amount:

30 times the genome size

Turnaround Time:

The standard turnaround time for the workflow, only including standard bioinformatics analysis, is ~55 work days for one sample.

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