Services Offered

Comprehensive epigenomic analysis using next-generation sequencing technologies


Chromatin Immunoprecipitation sequencing (ChIP-seq) is a technique for using the base sequence of DNA fragments isolated through chromatin immunoprecipitation to identify sites on the genome subject to histone modifications or DNA-protein interaction sites such as transcription factors.
Chromatin immunoprecipitation coupled with the utilization of next-generation high-throughput sequencing allows for thorough and highly accurate analysis.


High-throughput Sequencing Analysis Using Illumina HiSeq 2500

  • A sequence library is created from ChIPed DNA fragments (double strands) provided to us, and the base sequences are identified.
  • In addition to ChIP-Seq, MBD-Seq (Methylated DNA enriched using MBD2 protein) is also possible.

Bioinformatics Analysis

  • Data are mapped to a reference genome using CLC Genomics Workbench, and the mapped sequences can be visualized together with such elements as known gene arrangements.
  • A report listing identified binding sites, identified peak regions, and nearby known genes is generated.

Below is an example of how identified peak regions are displayed in CLC Genomics Workbench
(as shown below in the box with the dashed line) and a sample report.

In the report shown above, various parameters used to analyze binding sites such as false discovery rate (FDR), normalized difference and P-value, and information about nearby genes are displayed.

Analysis Workflow

Delivered data

  • Sequencing data (Base sequence information in text format following base-calling and quality assessment data)
  • Genome-mapping data (All sequences information mapped to a reference genome)
  • Annotation data (Information about genes located nearby identified peak regions)
  • CLC Genomic Workbench (Analysis results generated by CLC bio’s sequence analysis tool)
  • Quality Report (Results of quality check of sequence library and sequencing data)
  • Please contact us to discuss other result formats.