Department of Genetics

Epigenomics Core


The Epigenomics Shared Facility (ESF), part of Einstein’s Center for Epigenomics and an Illumina CSPro (certified service provider) laboratory, offers massively-parallel sequencing (MPS) including fully-automated library preparation, quality control and assurance, and a number of assays to study the epigenome. The high-throughput molecular technological resources in the ESF include massively parallel sequencing (MPS) platforms Illumina HiSeq2500, Illumina NEXTSeq500, Illumina MiSeq, Roche FLX; and TECAN freedom Evo® 200 Robotics.  Sample information is uploaded through a web-based interface (WASP) prior to sample submission, allowing LIMS and automated primary analysis of the data generated using the WASP System software, and returning data through visualization and web links. Data analytical services are provided by the Computational and Statistical Epigenomics Group. We encourage novel research in a number of human diseases, with early emphases on cancer, neuroepigenomics, the epigenomics of infectious disease, aging research, diabetes and renal disorders.


Support for diverse assays to study the epigenome include:

  • Epigenomic profiling of open chromatin (ATAC-SEQ)
  • Chromatin immunoprecipitation assays
    • Massively-parallel sequencing-based (ChIP-Seq)
  • Genome-wide Cytosine methylation assay- (5-mC)
    • Massively-parallel sequencing-based HELP-Tagging
    • Whole genome Bisulphite sequencing (MethylC-Seq-WGSBS)
    • Targeted bisulfite sequencing (SeqCap Epi -Roche - Human/Mouse)
  • Genome-wide hydroxymethylation analysis (5-hmC)
    • Massively-parallel sequencing-based (HELP-GT)
    • Oxidative bisulfite sequencing (oxBS-Seq)
  • Directional RNA-Seq, Targeted RNA-Seq, miRNA-Seq
  • Ultra Low RNA-Seq
  • Single Cell DNA/RNA-Seq (Single cell Genomics Core)
  • Exome Capture Enrichment Sequencing (Human/Mouse) and Targeted Resequencing
  • Whole-genome de novo or Resequencing and Amplicon-Resequencing

The services will include library preparation and sequencing plus Data Storage, primary data return, analysis and visualization through WASP ( DNA/RNA isolation services are also provided through Molecular Cytogenetic Facility. Secondary analysis is provided on request through Computational Genomics Facility. We are available on Science Exchange as well.


Please visit our available assays page for pricing or contact the core director.


Price Center Room 159


Faculty Advisor
John Greally, M.B., PhD

Shahina Maqbool, Ph.D.


Selected Publications

  • Thompson RF, Suzuki M, Lau KW, Greally JM. A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. Bioinformatics. 2009. doi:10.1093/bioinformatics/btp382 [PMID: 19561019].
  • Oda M, Glass JL, Thompson RF, Mo Y, Olivier EN, Figueroa ME, Selzer RR, Richmond TA, Zhang X, Dannenberg L, Green RD, Melnick A, Hatchwell E, Bouhassira EE, Verma A, Suzuki M, Greally JM. High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res. 2009;37(12):3829-39.
  • Figueroa ME, Melnick A, Greally JM. Genome-wide determination of DNA methylation by Hpa II tiny fragment enrichment by ligation-mediated PCR (HELP) for the study of acute leukemias. Methods Mol Biol. 2009;538:395-407.
  • Figueroa ME, Wouters BJ, Skrabanek L, Glass J, Li Y, Erpelinck-Verschueren CA, Langerak AW, Löwenberg B, Fazzari M, Greally JM, Valk PJ, Melnick A, Delwel R. Genome-wide epigenetic analysis delineates a biologically distinct immature acute leukemia with myeloid/T-lymphoid features. Blood. 2009;113(12):2795-804.
  • Oda M, Greally JM. The HELP assay. Methods Mol Biol. 2009;507:77-87.
  • Thompson RF, Reimers M, Khulan B, Gissot M, Richmond TA, Chen Q, Zheng X, Kim K, Greally JM. An analytical pipeline for genomic representations used for cytosine methylation studies. Bioinformatics. 2008;24(9):1161-7.
  • Gissot M, Choi SW, Thompson RF, Greally JM, Kim K. Toxoplasma gondii and Cryptosporidium parvum lack detectable DNA cytosine methylation. Eukaryot Cell. 2008;7(3):537-40.
  • Greally JM. Genomics: Encyclopaedia of humble DNA. Nature 2007;14;447(7146):782-3.
  • Glass JL, Thompson RF, Khulan B, Figueroa ME, Olivier EN, Oakley EJ, Van Zant G, Bouhassira EE, Melnick A, Golden A, Fazzari MJ, Greally JM. CG dinucleotide clustering is a species-specific property of the genome. Nucleic Acids Res. 2007;35(20):6798-807.
  • Gissot M, Kelly KA, Ajioka JW, Greally JM, Kim K. Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii. PLoS Pathog. 2007;3(6):e77.
  • Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E, Figueroa ME, Glass JL, Chen Q, Montagna C, Hatchwell E, Selzer RR, Richmond TA, Green RD, Melnick A, Greally JM. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 2006;16(8):1046-55.
  • Fazzari MJ and Greally JM. Epigenomics: beyond CpG islands. Nature Rev. Genet. 2004;5:446-455.

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