The Genomics Resources Core Facility (GRCF) at Weill Cornell Medicine (WCM) was established in the year 2000 and provides genomics technologies and related high throughput technologies to the basic and translational research and clinical communities including WCM, New York Presbyterian Hospital, Hospital for Special Surgery and external collaborators. The full-range and high quality of Next Generation Sequencing (NGS) services include experimental design, sample manipulation, instrumentation, data analysis/interpretation and validation. The goal of the GRCF is to provide cutting-edge high-quality services at affordable costs to the entire research community.
Instrumentation and Services
Currently GRCF contains NGS sequencers - Illumina NovaSeq 6000, NextSeq2000, NextSeq500 and MiSeq. Those instruments enable effective throughput scaling to suit virtually any study need and provide investigators with the throughput, speed, and flexibility to complete projects faster and more economically. The major workflow for the services and instruments is listed in the following table. During consultation, core staff will provide options and recommend the optimal experimental strategy.
Single-cell sequencing systems: Droplet-based single-cell system like 10X Genomics Chromium platform has been installed in the GRCF. It allows researchers to choose single cell sequencing methods as needed, such as RNA-Seq, ATAC-Seq and TCR/BCR, etc. Besides single-cell isolation/barcoding, library preparation and sequencing, GRCF also supports single-cell data analysis from aligning reads against reference genomes, identifying and counting the cell barcodes and UMI (Unique Molecular Identifier) for each read to report results.
Genomics data storage, management and bioinformatics support: GRCF maintains a comprehensive bioinformatics resource consisting of two highly qualified bioinformaticians who are available to assist campus researchers in all aspects of genomic data analysis. The high performance computing resources installed in GRCF are available for data cluster, storage and management. The in-house data analysis pipelines involve 1) Primary data analysis: including image acquisition, base calling, sample demultiplexing and raw fastq data generation. 2) Secondary data analysis: pre-alignment QC, sequence alignment, sequence assembly and post-alignment QC. 3) Tertiary data analysis: This is application specific analysis including gene expression profiling, differential expression analysis, alternative splicing detection, gene fusion detection, mutation detection and copy number detection, etc.
iLab system: http://wcmc.corefacilities.org/account/login
Experimental design, sequencing depth calculation, budget plan, sample extraction and submission related technical issues and strategies.
Sample quality control
Agilent 2100 Bioanalyzer, Agilent 4200 TapeStation, Thermo Fisher Scientific NanoDrop 8000 Spectrophotometer, and Qubit Fluorometer; Life Technologies Quantstudio 6 Flex real-time PCR
QC for both DNA and RNA samples from different sources.
Library construction (manual and robot)
Agilent NGS workstation Bravo B, Eppendorf epMotion 5075m automated liquid handling Robot
RNA-Seq, Capture-based RNA-Seq, miRNA-Seq, ChIP-Seq, WGS, WES, Customized Panel-Seq.
Next generation sequencing
Illumina NovaSeq6000, NextSeq2000, NextSeq500, Miseq
Single-end Sequencing, Pair-end Sequencing.
Data analysis, storage and management
In house data servers, Amazon AWS Glacier Deep Archive
Primary, secondary and tertiary data analysis; Amazon Web Services – a S3 Glacier Deep Archive cloud system for a long-term solution for data deliver, store and management.
Offering support letter and writing genomics part for PIs’ grant and manuscript preparations.
Laboratory Information Management System (LIMS)
Agilent iLab System
For user registration, sample submission, tracking and billing.
Core Contact: Jenny Xiang, M.D.
Phone: (212) 746-4258 (O), (212) 746-6238/5076 (Lab)
Monday - Friday
9:00 AM - 5:00 PM