Epigenomics Shared Facility


The Epigenomics Shared Facility (ESF) is a part of Einstein’s Center for Epigenomics and an Illumina CSPro (certified service provider) laboratory. The high-throughput molecular technological resources in the ESF include massively parallel sequencing (MPS) platforms: the Oxford Nanopore MinION,  Illumina NEXTSeq500, Illumina HiSeq2500 and Illumina MiSeq; supported by TECAN freedom Evo® 200 Robotics.  The core facility space is dedicated and customized, with MPS library preparation performed in a positive-pressure room isolated from the post prep and sequencing room. The MPS machines are connected by high-bandwidth networking to dedicated computing equipment located in a server room.

Sample submission is coordinated through a laboratory information management system (LIMS) component of the WASP (an integrated LIMS and batch processing system: http://waspsystem.einstein.yu.edu).  WASP allow users for electronic submission of their samples, real-time follow-up of the pipeline and access to the data once available. The facility has a turnaround of 2 to 3 weeks per library/job/project. The data is backed-up and available for at least 6 months on the WASP server from the Albert Einstein College of Medicine.

The ESF supports diverse assays for MPS analysis and strives to bring cutting-edge technologies to benefit the programs of Einstein researchers. Recently, with the current COVID-19 pandemic, ESF is ready to facilitate and support your research into the SARS-CoV-2 and the search for effective diagnostics and therapies to cure COVID-19. Please check the Epigenomics Shared Facility -COVID-19 overview for details.


A.    The ESF is now providing support and services for long read sequencing utilizing Oxford Nanopore’s MinION platform.

  • Direct RNA sequencing: transcriptome and epitranscriptome (RNA modifications) analysis using the MinION platform.
  • Direct cDNA Sequencing (For Low Input samples)
  • Genomic DNA sequencing (Ultra-long reads - up to 2 Mb)
  • Amplicons sequencing
  • Single-cell RNA sequencing combining 10x Chromium  and  Nanopore technology for longer reads.

B.    Support for diverse assays for short read sequencing to study the epigenome include:

  • Epigenomic profiling of open chromatin (ATAC-SEQ)
  • Chromatin profiling assays
  • Cleavage Under Targets and Release using Nuclease (CUT&RUN-Seq)
  • Chromatin immunoprecipitation assays
  • Massively-parallel sequencing-based (ChIP-Seq)
  • Methylated DNA immunoprecipitation sequencing (MeDIP/hMeDIP-Seq)
  • Genome-wide Cytosine methylation assay- (5-mC)
  • Massively-parallel sequencing-based HELP-Tagging
  • Whole genome Bisulphite sequencing (MethylC-Seq-WGSBS)
  • Enzymatic Methyl-seq (EM-seq)
  • Reduced Representation Bisulfite Sequencing (ERRBS-Seq)
  • 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 ATAC-Seq
  • Exome Capture Enrichment Sequencing (Human/Mouse) and Targeted Resequencing
  • Whole-genome de novo or Resequencing and Amplicon-Resequencing  

The services include library preparation and sequencing plus Data Storage, primary data return, analysis and visualization through WASP (http://waspsystem.einsteinmed.edu). DNA/RNA isolation services are also provided through Molecular Cytogenetic Facility. We are available on Science Exchange as well.
Secondary analysis is also provided on request through our Computational and Statistical Genomics/Epigenomics Groups (http://wasp.einstein.yu.edu/index.php/AnalysisRequest). We are available on Science Exchange as well. Pricing information is also available through WASP: http://waspsystem.einsteinmed.edu/ws/auth/sequencingPricing.do.



Scientific Director
John M. Greally, M.B., Ph.D.

Operations Director
Shahina B. Maqbool, Ph.D.

Location and hours of operation

Hours Location

M-F, 9-5 

Price Center, Room 159

Links and Resources

  1. WASP
  2. Epigenomics Webpage
  3. New York Genome Center


Name Role Phone Email Location
Shahina B. Maqbool, Ph.D.
Operations Director
Price Center 159

Service list

Search available services: View: by category alphabetically
Assays (68)
Illumina MiSeq Sequencing Services (10)
Illumina HiSeq 2500 Sequencing Services (2)
Automated Library Preparation For Massively Parallel Sequencing (24)
Library Preparation For Massively Parallel Sequencing (9)
NextSeq Sequencing Services (7)
Multiplexing Charges (6)
WASP (1)
Custom Design Target Capture Sequencing (5)
SeqCap Epi (1)
Adaptors and Primers (3)
Whole Human Genome Sequencing (1)
Other (6)
Archived Services (46)