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Single Cell Biology

Cold Spring Harbor's Single Cell Biology Core Facility brings cutting-edge single cell technologies to collaborators both inside and outside of the Laboratory. We currently specialize in single cell transcriptomics, and offer assistance in a variety of gene expression workflows based around the 10X Genomics platform.

External Links

Cold Spring Harbor Laboratory

CSHL Cancer Center Shared Resources

Key Services:


10X Genomics Visium Spatial Transciptomics

  • Spatially resolved whole-transcriptome analysis

  • 6.5 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

  • Resolution of 1-10 cells

  • Spot width 55uM, center-to-center distance 100uM (higher resolution coming soon with Visium HD


10X Genomics Xenium Spatial Transciptomics

  • Spatially resolved transcriptome data @ subcellular resolution

  • 300-500 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


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




10X Genomics Single Cell 5' Gene Expression

Enables Single Cell 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

DALL·E 2024-02-23 19.23.29 - Create a cartoon diagram of a cell that displays both RNA and

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


Plate Based 3’ Well Barcoded Low Input RNA-seq:

​Up to 96 Samples per library of well barcoded RNAseq 

You provide one of the following:

  • 15 ul of purified RNA at 25 ng/ul or more per sample

  • 96 well plate of cells frozen in lysis buffer 


  • Perform Well-Barcoded RT reaction + cDNA pooling

  • Sequence using the Illumina NextSeq platform

  • Deliver FASTQs, BAM files, gene counts matrix

Frozen Nuc-Seq

  • Fresh or flash-frozen tissue

  • On-site FACS sorting & direct-to-10X workflow


Contact Us

500 Sunnyside Blvd

Woodbury, NY 11797


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