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Single-Cell Biology

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The Single-Cell Biology Shared Resource provides access to facilities, equipment, and expertise for the study of gene expression, protein abundance, and genetic alterations at single-cell resolution. We offer expert-level, quality-controlled service for challenging applications single cell and spatial applications, and can provide assistance with every stage of a single-cell experiment, including study design, tissue dissociation, cell culture, population enrichment, cell sorting, quality control, and library preparation, and data analysis.

To inquire about a single-cell project idea, contact Jon Preall.

EXTERNAL USERS: Many CSHL Core Facility Services are also available to external users, both academic and non-academic, and can be accessed through iLab. Please reach out to individual core directors for more information on services, rates and how to access.

Shared Resource Staff

Resource Head

Jessica Tollkuhn, Ph.D.
tollkuhn@cshl.edu

Head of Genomics Technology Development

Jonathan Preall, Ph.D.
516-422-4086
jpreall@cshl.edu

Staff

Claire Regan, Analyst
cregan@cshl.edu

Evan Zhang
ezhang@cshl.edu

Lauren Ward
lward@cshl.edu

Explore all the CSHL Core Facilities

10X Genomics Single Cell Flex (Fixed RNA Profiling)

  • Up to 128,000 cells per lane across up to 16 samples
  • Probe-based RNA profiling
  • Batch together samples collected and fixed at different times or from FFPE tissue blocks.
  • Lowest cost per sample

10X Genomics Single Cell 3’ Gene Expression

  • 2,000-20,000 cells per lane
  • Oligo-d(T) primed, 3′-biased digital gene expression
  • Best option for pure expression profiling

Add-ons:

  • CITE-Seq / Feature Barcoding
  • CRISPR guide capture
  • Cell Hashing / CellPlex multiplexing

10X Genomics Single Cell 5′ Gene Expression / Immune Profiling

  • Paired TCR alpha- and beta chain V(DJ) sequencing
  • Paired BCR heavy and light chain V(DJ) sequencing
  • Combined Immune Profiling 5’-Gene Expression
  • BEAM:(Bar-Enabled) Antigen Mapping
    • Identify B- or T-cell clones binding to a labeled antigen

10X Genomics Single Cell ATAC-seq

  • Genome-wide Chromatin Accessibility in single cells
  • 2,000-8,000 cells per lane
  • Promoter / enhancer accessibility
  • Motif enrichment / discovery

10X Genomics Multiome ATAC + Gene Expression

  • 2,000-8,000 cells per lane
  • Paired 3’ nuclear gene expression and chromatin accessibility from single cells
  • Analyze relationships between regulatory motifs and gene expression in multiple lineages simultaneously

10X Genomics Visium Spatial Transciptomics

  • Spatially resolved whole-transcriptome analysis
  • 5 x 6.5 mm or 11 x 11 mm formats
  • Starting Matrials:
    • Fresh Frozen OCT embedded tissue
    • FFPE blocks
    • Hard-mount FFPE, H&E-stained slides
  • Two resolutions:
    • SD – Spot width 55um, center-to-center distance 100um
    • HD – 2 um grid binned into 2um, 8um or 16 um bins

10X Genomics Xenium Spatial Transcriptomics

  • Spatially resolved transcriptome data @ subcellular resolution
  • 300-500 and 5000 gene panels
  • 2 slides per run, 1cm x 2cm imageable area each
  • Start from Fresh Frozen OCT or FFPE blocks
  • Premade + add-on and fully custom gene panels
  • Panel design assistance service

Lunaphore COMET multiplexed IF

  • 40-plex protein immunofluorescence imaging
  • 2 antibodies per cycle, 555/647

Spatial Multiomics

  • Combine Xenium, Visium, COMET services on a single or adjacent sections
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