Single-Cell Biology

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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 Visium Spatial Transcriptomics. Profile gene expression from fresh or frozen tissue sections with ~100um resolution. Detailed transcriptomic signatures from ~5,000 array spots per tissue slice can be deconvoluted to determine cellular composition and unique gene expression profiles within each spot. Combine with up to 4-color immunofluorescence microscopy to visualize nuclei and protein markers of interest. Inquire with the Core to plan your spatial transcriptomics experiment.
  • 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.

Explore all the CSHL Core Facilities

Shared Resource Staff

Head of Genomics Technology Development

Jonathan Preall, Ph.D.

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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.