Next Generation Genomics

The Next Generation Genomics Shared Resource provides access to high throughput Next Generation Sequencing (NGS) technologies and to full service Sanger DNA sequencing using fluorescence-based technology. The Shared Resource is currently developing services to offer gene expression profiling and other genomics readouts from heterogeneous tissue samples at single-cell resolution. In combination, the Resource offers cutting-edge technology along side convenient in-house services for a broad range of genetic analysis. For more information see below or contact the Resource Director, Dick McCombie, Ph.D.

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Shared Resource Staff

NGS Project Manager

Sara Goodwin, Ph.D.

Head of Genomics Technology Development

Jonathan Preall, Ph.D.

The Woodbury Genome Center is home to the latest in both short and long read sequencing technology. Our high-throughput sequencing technology offers a broad range of applications including:

  • De novo genome sequencing/genome re-sequencing
  • Whole genome or targeted methylation analysis
  • Targeted sequencing using hybrid selection (i.e. exome and panel sequencing)
  • siRNA and small RNA sequencing
  • ChIP-Seq and RIP-Seq
  • RNA-Seq


The facility houses a suite of Next Generation Sequencing equipment. The core currently operates one Illumina HiSeq2500, two Illumina NextSeq500s, one NextSeq 550 and one Illumina MiSeqs, which can be used to produce more than 4 trillion bases (Tb) in reads each month.

The Core also contains one Pacific Biosciences RSII sequencer which generates reads in excess of 30kb and yields up to 1 billion bases (Gb) per SMRTcell. The Pacific Biosciences Sequel instrument in the facility can generate ~6Gb per SMRTcell. Together, these Pacific Biosciences instruments can generate ~250 Gb of long reads a month.

The Core also houses six Oxford Nanopore MinIONs, 1 Oxford Nanopore GridION and 1 Oxford Nanopore PromethION. Currently our nanopore pipeline can generate up to 50 0Gb of long read data a month. However, this is expected to increase dramatically as we implement PromethION optimizations.

Please contact the Next Generation Genomics Core at nextgenseq@cshl.edu for consultation on applications, experimental set-up, strategies for experimental design, and library preparation requests.

Cold Spring Harbor Lab’s Single Cell Core Facility has a technology development mission, and is eager to work with clients to develop new assays and techniques. The facility is currently working in a ‘beta-testing’ stage to offer gene expression profiling and other genomics readouts from heterogeneous tissue samples at single-cell resolution. Our capabilities are routinely expanding, and we are happy to discuss new ideas with potential clients and decide how to proceed.

The facility is equipped with the latest technology including:

  • 10X Genomics Chromium controller, which is capable of capturing up to ~80,000 individually barcoded cells in a single run. 10X Genomics currently offers multiple single-cell applications: total mRNA expression profiling, human T-cell receptor V(D)J sequencing and Human B-cell V(D)J sequencing. This technology has proven to be a powerful tool for discovering novel rare cell populations, for characterizing developmental changes in gene expression within cell lineages, or to uncover subtle transcriptional responses to perturbations in select cells amid a heterogeneous mixture.
  • Fluidigm C1 Single Cell autoprep system, which captures and processes a smaller number of cells than the 10X Genomics platform (chip sizes range from 96 to 800 chambers), but the customizable microfluidic circuits enable a wide variety of downstream analyses and greater resolution per-cell The Fluidigm C1 can be programmed to generate sequencing libraries capturing full-length mRNA, epigenetic readouts such as ATAC-Seq, alternative transcription start sites via CAGE-seq, as well as other user-designed and validated protocols.
  • Sony SH800 Cell Sorter, which is a 4-laser, 6-channel FACS instrument with auto-calibration and disposable microfluidics. It is capable of bulk sorting up to two populations simultaneously into collection tubes or 96- and 384-well plates. Single cell and single nuclei sorting with downstream genomics applications will be made available as per the user’s needs. Users will have the option of giving samples to the Core for sorting and analysis, or to receive training and run their own samples.

Have a project idea? Contact us!

We are currently seeking a limited number of beta-test partners to provide tissue samples along with an idea of the target cell subpopulations to be enriched prior to single cell capture and sequencing. If desired, the single-cell core facility will work closely with clients to develop optimal tissue isolation, handling, and dissociation protocols, as well as cell sorting.

Contact Jon Preall to get started.

The DNA Sequencing Shared Resource provides cost effective and rapid DNA sequence analysis using an ABI3730 instrument. The DNA Sequencing Facility offers full service fluorescent-based capillary DNA sequencing. Users can submit samples of PCR products, single and double stranded plasmids, BACs and cosmids. Facility staff set up reactions, run the samples and post final data on a shared drive for retrieval. The resource also provides consulting expertise for DNA preparation to improve the DNA sequencing results of the users. The on-site service provides convenience and a rapid turn-around time, facilitating the many projects that require DNA sequencing support.

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Cold Spring Harbor Laboratory is an NCI-designated Cancer Center. As a basic research institution, CSHL does not treat patients. Information about individual cancers is available at the NCI CancerNet. Questions about CSHL’s cancer research program should be directed to our Public Affairs Department.