Department of Genetics

Epigenomics Core


To facilitate the research programs of Einstein investigators by providing shared resources to study epigenetic modifications across the entire genome, including DNA methylation, histone modification and DNA-protein interactions.

This shared facility is part of Einstein’s Center for Epigenomics.


  • Massively-parallel sequencing (MPS)
  • Platforms
    • Illumina GA2 (Solexa)
    • Roche FLX (454)
  • Assays
    • ChIP-seq
    • HELP-tagging
    • MicroRNA-Seq
  • MPS services provided through Genomics Core 
    • Whole-genome de novo or Resequencing
    • Digital expression profiling/tag profiling
    • RNA-seq

The services will include library preparation, sequencing, primary data analysis and visualization. 

  • Long oligonucleotide microarrays
  • Platform
  • Assays
    • ChIP-chip
    • HELP
    • CGH
    • Gene Expression
    • Affymetrix provided through Genomics Core  

Services will include sample labeling with Cy5 and Cy3 fluorophores, hybridizations, primary data analysis and visualization. Following initial hybridizations, the arrays can be stripped and re-used. 

  • Sequenome EpiTyper quantitative DNA methylation analysis provided through Genomics Core 

Services are accessible through our wikilims resource, which provides detailed information about the sample requirements, specific protocols and sample submission request forms.

Data Analysis:
Data are accessible through the wikilims resource.

For MPS services, sequence reads will be processed and aligned against a reference genome and processed using the appropriate data analysis pipeline for that assay. We deliver summary and quality metric data along with the sequencing data.

For microarray services, hybridized arrays will be scanned and converted into pair files after aligning with the design files using NimbleScan 2.5. Further analysis will be performed to visualize the data. We deliver summary and preliminary analysis reports and statistics along with the pair files.

Assistance with retrieving data, instructions as to how to use the tools and more extensive data analysis on a fee-for-service basis are provided by the Computational Genomics Core (Link to the Computational Genomics Core).

Analytical Resources:
Analytical resources are available to Einstein researchers at the Analytical Tools website maintained by the Computational Genomics Core. This site includes Roche-Nimblegen software: NimbleScan 2.5 and SignalMap 1.9, CLC Genomics Workbench, Ingenuity Pathway Analysis, R/BioConductor and more.


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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