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Genomics Core

Genomics and Epigenomics Core Facility

 

Summary

The Genomics and Epigenomics Core Facility of the WCM Core Laboratories Center (CLC) provides state-of-the-art instruments and services, and expertise in their applications, to the Weill Cornell Medicine (WCM) community and to outside investigators.  Resources and services include next generation sequencing, epigenomic assays, single cell genomics, nucleic acid mass spectrometry, and real-time PCR.  The facility provides consultation on project design and data analysis, and offers seminars, educational workshops and training.

 

Overview

History:  The WCM CLC Genomics and Epigenomics Core Facility is the product of an ongoing integration of two previously separate core facilities, the Genomics Resources Core Facility (established in 2000) and the Epigenomics Core Facility (established in 2008). 

Location:  The core is located on the 1st and 4th floors of the “A” building and the 5th floor of the “C’ building at 1300 York Avenue, New York, NY.  

WCM Core Laboratories Center (CLC):  The WCM CLC was established in 2015.  The CLC includes core facilities that offer resources and services in genomics and epigenomics, proteomics and metabolomics, flow cytometry, imaging (e.g., optical and electron microscopy, high content screening, MRI, PET/CT, and ultrasound), synthetic and analytical chemistry, and nuclear magnetic resonance (NMR).

Open to all:  The resources and services of the core facility are open to all investigators at Weill Cornell Medicine, Cornell University and Cornell-affiliated institutions.  The facility also provides services to external investigators at both academic institutions and commercial enterprises.

Services

Next Generation Sequencing-

Epigenomics:

NGS epigenomics applications include (1) DNA methylation profiling, including whole genome bisulfite sequencing (WGBS), targeted methylome sequencing, enhanced reduced representation bisulfite sequencing (ERRBS), genome wide detection of 5-hydroxymethylcytosine modification (5hmC-BIC-seq); (2) assessment of the functional state of chromatin by assaying for transposase activity (ATAC-seq); and (3) genome wide protein-nucleic acid association mapping by chromatin immunoprecipitation sequencing (ChIP-seq).

Genomics:

NGS genomics applications include exome capture, whole genome and targeted region de novo sequencing and resequencing, targeted region and whole transcriptome profiling, small RNA analysis, and metagenomics projects.

Single Cell Genomics and Epigenomics

The core offers strong support for single cell genomics and epigenomics projects with a 10X Genomics Chromium system, a Drop-seq instrument, a BioRad/Illumina ddSEQ Single-Cell Isolator, access to a Fluidigm C1 single-cell auto prep platform, and close collaboration with the CLC Flow Cytometry Core Facility.

Epigenomics assays

Nucleic acid mass spectrometry

The core offers the Agena Bioscience (Sequenom) Compact MassArray system, a platform that uses MALDI-TOF mass spectrometry to measure PCR-derived amplicons.  Currently used for methylation analysis; other applications include genotyping and mutation detection, gene expression analysis, and pathogen detection. 

Real-time PCR

An Applied Biosystem QuantStudio 6 Flex Real-Time PCR System (384-well and 96-well) uses a fluorescence detection method for quantitative and qualitative analysis of nucleic acid sequences including gene expression, regulation and variation. This system is compatible with SYBR and TaqMan assays as well as several other dye assays.  It can detect as small as a 1.5 fold change with 10 logs of linear dynamic range. 

Sanger Sequencing & Fragment Analysis

The core offers a sample “drop and ship” location and an express mail service to facilitate WCM investigators’ access to Sanger sequencing and fragment analysis services done on two ABI 3730xl DNA Analyzers in the Cornell Biotechnology Resource Center (BRC) Genomics Facility, located on the Cornell University campus in Ithaca, NY.  All orders must be placed online.  Once you have placed your order, you will receive an order number.  Sample preparation instructions are available online.  Send your samples in unpadded, labeled envelope.  Write your order number, name, telephone number, and lab location on the envelope.  Drop off the sealed, labeled envelope containing your samples in the DNA Sequencing Drop-Off Box, located in the basement corridor of the B building (near the mail room by the Federal Express drop box) at 1300 York Avenue, New York, NY.  Samples are sent overnight by Federal Express to the BRC Genomics Facility on the Cornell Ithaca campus, with shipments leaving New York every Monday through Thursday, at 4:30 pm (except on institutional holidays).  

 

Consultation

Seminars, workshops and training

Resources

Next Generation Sequencing:  Five Illumina NGS instruments, including HiSeq 4000, two HiSeq 2500/1T, NextSeq 500, and two MiSeq.  

Single Cell Genomics and Epigenomics: 10X Genomics Chromium, BioRad/Illumina ddSEQ Single-Cell Isolator, custom built Drop-seq instrument, access to Fluidigm C1. 

Nucleic Acid Mass Spectrometry: Agena Bioscience Compact MassArray.  Real-time PCR: ABI 7900 HT Sequence Detection System. 

General: Covaris E220 Evolution, 2 Agilent 2100 Bioanalyzers, Agilent Tape Station, 2 Nanodrop1000 spectrophotometers, 2 Qubit fluorometers, Glomax/BioTek plate reader, Gel Logic 200 Imaging System, 3 liquid handling robots (Eppendorf epMotion 5075m, Agilent Bravo B, Perkin Elmer Zephyr, Hamilton Starlet).

Contact Information

Jenny Xiang, M.D.
Director of Genomics Services
WCM CLC Genomics and Epigenomics Core Facility
(212) 746-4258
jzx2002@med.cornell.edu

 

Alicia Alonso, Ph.D.
Director of Epigenomics Services
WCM CLC Genomics and Epigenomics Core Facility
(212) 746-3260
ala2035@med.cornell.edu

 

Doron Betel, Ph.D.
Director of Informatics Services
WCM CLC Genomics and Epigenomics Core Facility
(646) 962-5602
dob2014@med.cornell.edu

More Information

For more information about all services and pricing, to register as a user of the core, and/or to submit samples, please go to the WCM iLab portal at http://wcmc.corefacilities.org.

For detailed information about the core’s epigenomics services, please go to http://epicore.med.cornell.edu.

Contact Information

Core Contact: Jenny Xiang, M.D.

Email: jzx2002@med.cornell.edu

Phone: (212) 746-4258