About

Epigenomics Shared Facility

Overview

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 NEXTSeq 2000, and Illumina MiSeq; supported by TECAN Freedom Evo® 200 Robotics; and also includes the BD Rhapsody HT Xpress system from Waters Biosciences (formerly BD Biosciences) for single-cell multi-omic assays. 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 (Agilent SLIMS), a component of iLab (an integrated LIMS and batch processing system).  SLIMS allows users to electronically submit their samples, follow the pipeline in real time, and access the data once available. The facility has a turnaround of one to two weeks per library/job/project. The data is backed up and available for at least six months on the Albert Einstein College of Medicine server. The ESF supports diverse assays for MPS analysis and strives to bring cutting-edge technologies to benefit the programs of Einstein researchers.

SERVICES:

A. The ESF is now providing support and services for single-cell assays, expanding the library of multi-omic assays on the BD Rhapsody HT Xpress system (Waters Biosciences) for fragile, rare, and challenging cell types such as:

    • Neutrophils
    • Eosinophils
    • Basophils
    • Microglia

Services Include:

Assays for mRNA Expression:

  • Single-Cell Whole Transcriptome (scWTA) Analysis — an unbiased approach to assay all poly-A transcripts, with the ability to capture transcript variants.
  • Single-Cell Targeted Transcript Amplification Analysis — uses a set of transcript-specific primers to precisely amplify genes of interest. This requires 10 times fewer reads than WTA.
  • Single-Cell Whole Transcriptome (scWTA-SMK) Analysis using BD Rhapsody Sample Tag (multiplexing antibodies) —this increases throughput per lane of cartridge, lowers reagent costs, reduces batch effects, and helps identify and remove multiplets.

Assays for Epigenomics/Multi-omics:

  • Single-Cell ATAC-seq
  • scATAC-seq + SMK (Sample Tag multiplexing)
  • scATAC-seq + mRNA (scWTA)
  • scATAC-seq + mRNA (scWTA) + SMK (Sample Tag multiplexing)
  • scCUT&Tag-seq

Please contact the facility if you are interested in any of the following assays:

  • BD Rhapsody™ TCR/BCR (VDJ or VDJ CDR3 Assays), intracellular/extracellular CITE-seq single or multi-omic assays alongside scWTA or targeted mRNA expression and protein analyses.
  • BD Rhapsody™ long-read sequencing for Oxford Nanopore or PacBio to capture full-length transcript information.

B. 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)
    • Amplicon sequencing
    • Single-cell RNA sequencing for longer reads.

C. Support for Diverse Assays for Short-Read Sequencing to Study the Epigenome

Support includes the following assay categories:

  • 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 Assays (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)
  • RNA Sequencing
    • Directional RNA-seq
    • Targeted RNA-seq
    • miRNA-seq
    • Ultra-Low RNA-seq
  • Exome & Targeted Sequencing
    • Exome Capture Enrichment Sequencing (Human/Mouse)
    • Targeted Resequencing
  • Genome Sequencing
    • Whole-Genome De Novo or Resequencing
    • Amplicon Resequencing
  • Integrated Approaches
    • Blended Genome Exome-seq (BGE-seq)

D. Support for AlloSeq Tx17 (HLA Genotyping)

The ESF is now providing support and services for rapid, high-throughput Human Leukocyte Antigen (HLA) typing using innovative hybrid capture and massively parallel sequencing. 

Please enquire.

 

The ESF is located on the 1st floor of the Price Building and is always happy to consult with interested researchers and advise on the best ways to help advance scientific discoveries at Einstein and beyond. Services are priced competitively and are available through iLab, and include library preparation and sequencing, plus data storage, primary data return, and analysis. DNA/RNA isolation services are also provided through the Molecular Cytogenetics Facility. We are available on Science Exchange and iLab.

Secondary analysis is also provided on request through our Computational Genomics Core (CGC).

Please contact the facility if you are interested in any of these assays or would like to learn more about how the ESF can support your work.

Leadership

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. Epigenomics Webpage
  2. New York Genome Center

 

*Please acknowledge the Research Resource Identifiers (RRIDs) SCR_023284 in any publication that was supported by use of this shared resource.*

Contacts

Name Role Phone Email Location
Shahina B. Maqbool, Ph.D.
Operations Director
 
718.678.1163
 
shahina.maqbool@einsteinmed.edu
 
Price Center 159
 

Service list


Search available services: View: by category alphabetically
► Assays (118)
► BD Rhapsody Single Cell (10)
► Illumina MiSeq Sequencing Services (13)
► Automated Library Preparation For Massively Parallel Sequencing (24)
► Library Preparation For Massively Parallel Sequencing (7)
► Multiplexing Charges (6)
► WASP (1)
► Custom Design Target Capture Sequencing (6)
► SeqCap Epi (1)
► Whole Human Genome Sequencing (1)
► Other (4)
► NextSeq2K Sequencing Services (11)
► Tape Station (15)
► Archived Services (47)