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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 Single Cell 3’ Gene Expression

  • 2,000-8,000 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


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’ 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 transcriptome data

  • Analyze tissue sections up to 6.5 x 6.5 mm

  • Resolution of 1-10 cells

  • Spot width 55uM, center-to-center distance 100uM


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

​Up to 96 Samples per library of well barcoded RNAseq 

You provide:

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

  • Or 96 well Tissue Culture plate of cells frozen in lysis buffer 



  • Perform Well Barcoded RT reaction and prepare one library per plate

  • Sequence using the Illumina NextSeq platform

  • Perform primary analysis, mapping to a genome of your choice and return, FASTQs, bam files and a per sample gene counts matrix


  • Fresh or flash-frozen tissue

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


Add on Services

Antibody-based proteogenomics

Custom amplicon enrichment

Contact Us

500 Sunnyside Blvd

Woodbury, NY 11797


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