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

We:

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