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Epigenomics Core Laboratory

Services

The Epigenomics Core Laboratory produces hundreds of millions of short sequence reads of individual DNA molecules using the Illumina NextSeq 500 or Illumina's MiSeq platforms. It is led by the Acting Deputy Scientific Director and Deputy Chief of the Epigenetics and Stem Cells Biology Laboratory Paul Wade, Ph.D., and managed by Core Manager Gregory G. Solomon. We highly recommend you meet with our staff before submitting a project.

Background

What is NextGen Sequencing?

Next-generation sequencing applies to genome sequencing, genome resequencing, transcriptome profiling (RNA-Seq), DNA-protein interactions (ChIP-sequencing), and epigenome characterization. The high demand for low-cost sequencing has driven the development of high-throughput sequencing (or next-generation sequencing) technologies that parallelize the sequencing process, producing thousands or millions of sequences concurrently. High-throughput sequencing technologies are intended to lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods. In ultra-high-throughput sequencing millions of sequencing-by-synthesis operations may be run in parallel.

Illumina MiSeq Sequencer
An Illumina MiSeq sequencer.

In this method, DNA molecules and primers are first attached on a slide or flow cell and amplified with polymerase so that local clonal DNA colonies, later coined "DNA clusters," are formed. To determine the sequence, four types of reversible terminator bases (RT-bases) are added and non-incorporated nucleotides are washed away. A camera takes images of the fluorescently labeled nucleotides. Then, the dye, along with the terminal 3' blocker, is chemically removed from the DNA, allowing for the next cycle to begin. Unlike pyrosequencing, the DNA chains are extended one nucleotide at a time and image acquisition can be performed at a delayed moment, allowing for very large arrays of DNA colonies to be captured by sequential images taken from a single camera.

Types of projects we do:

  • Whole Genome Sequencing (WGS)
  • RNAseq (Transcriptome sequencing)
  • ChIPseq
  • Methylseq
  • Exome sequencing
  • Targeted re-sequencing

Run Formats:

  • Single end - typical run lengths are between 36bp to 150bp. We can do as large as 300bp for special samples.
  • Paired end - Reads from both ends of the strand. Typical read lengths are between 75bp and 150bp. We can do as large as 250bp for special samples.

Samples may be multiplexed from 2 to 96 samples per lane depending upon the amount of coverage needed and flow cell type used.

NIEHS Shared and Core Facilities are available to NIH researchers. Information for staff on utilizing these services may be found on the NIEHS Junction or by contacting the staff below.

Scientific Staff

Greg Solomon
Gregory G. Solomon
Manager
P.O. Box 12233
Mail Drop C3-03
Durham, N.C. 27709

Tel 919-541-1812
solomon1@niehs.nih.gov
Jason Malphurs
Jason A. Malphurs
Biologist
P.O. Box 12233
Mail Drop C3-03
Durham, N.C. 27709

Tel 919-316-4588
Fax 919-541-1898
malphurs@niehs.nih.gov
John Otstot
John T. Otstot
Biologist
P.O. Box 12233
Mail Drop C3-03
Durham, N.C. 27709

Tel 919-541-0493
otstot@niehs.nih.gov
Nicole Reeves, M.S.
Nicole Reeves, M.S.
Biologist
P.O. Box 12233
Mail Drop C3-03
Durham, N.C. 27709

Tel 919-541-0476
Fax 919-541-0146
reeves@niehs.nih.gov