EpiGnome/TruSeq DNA Methylation

  • Unlock small samples (50–100 ng DNA input)
  • CpG, CHH, & CHG regions included for comprehensive, whole-genome results
  • Fast protocol – five-hour method
  • Capture full sample diversity

Sequence the entire sample–no loss of information

The process of bisulfite treatment denatures genomic DNA into single stranded DNA. EpiGnome/TruSeq DNA Methylation* converts single stranded DNA into an Illumina sequencing library. All ssDNA fragments are captured into an Illumina sequencing library during the EpiGnome procedure, therefore eliminating the loss of diversity associated with other methods.

Seamless and supported analysis in the cloud

TruSeq DNA Methylation libraries can be aligned to the human genome and compared for differential methylation with Illumina BaseSpace Apps MethylSeq and MethylKit. These applications are fully supported and were developed specifically for TruSeq DNA Methylation library preparation.


Example data sets for TruSeq DNA Methylation libraries, also available in BaseSpace Sequence Hub (use the “Methyl Seq” category filter) demonstrate unparalleled quality and seamless analysis.

Deep coverage of critical genomic regions

Depth of coverage is enhanced in genomic areas with biological utility. EpiGnome/TruSeq DNA Methylation captures full sample diversity of critical areas, including:

  • Coding region start and end for exons from the canonical transcript of protein coding genes for genes known to be involved in cancer, taken from SOMA and CRUK panels (as well as literature-derived cancer genes)
  • Genes defined by the American College of Medical Genetics as being medically relevant (ACMG genes)
  • Exonic coding regions from Ensemble 70
  • List of 100 promoters defined by the Broad Institute as being of high interest and difficult to sequence

Whole genome bisulfite sequencing yields maximum methylation information

Whole genome bisulfite sequencing yields maximum methylation information
Reads Passing Filter 736,320,254
Paired-end alignments with unique best hit 537,880,874
#C nucleotides analyzed 14.9 billion
C methylated in CpG 54%
C methylated in CHG 1.9%
C methylated in CHH 0.9%
% Unique 9.19%

Methyl-Seq library was prepared from 100 ng Coriell GM18507 gDNA and sequenced on an Illumina HiSeq 2500 with paired-end 2x75 bp run length. Data from four lanes of the HiSeq flow cell were combined to achieve 21.5x genome coverage.

Whole genome methylation coverage of CpG, CHG, and CHH contexts

Whole genome methylation coverage of CpG, CHG, and CHH contexts
Total Read Coverage Green
Hypomethylated Regions (20-80% methylated) Grey
Hypermethylated Regions (>80% methylated) Blue
# Reads 736 m
Run lengths 2 x 75 bp
Avg. genome coverage 21.5x
Starting amount of Coriell GM18507 gDNA 100 ng
Reference genome UCSC hg19

DNA from beta-lymphocyte cells sequenced on an Illumina HiSeq 2500 and visualized across chromosome 22. EpiGnome/TruSeq DNA Methylation is highly sensitive, detecting low levels of CHG and CHH methylation below 2%.
The methylation patterns in the CHG and CHH contexts are shown on a greatly expanded scale to explore complexity.

Sensitivity detects regions of high and low methylation across genome

Sensitivity detects regions of high and low methylation across genome

CpG methylation pattern across a 10 Mb region of chromosome 1. CpG coverage is shown in green. Regions of high CpG methylation are shown in red and regions of low CpG methylation are shown in blue.

*The EpiGnome library preparation kit has been renamed TruSeq DNA Methylation. Kits with either name on the label contain the same quality reagents and follow the same workflow.

Library preparation with the TruSeq DNA Methylation kit requires bisulfite conversion reagents and FailSafe PCR enzyme to be purchased separately. Please see the library preparation guide for ordering information.

Catalog IDs: EGMK81312, EGMK91324, EGMK91396, EGIDX81312