CSHL Single Cell Biology Core
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
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
Add-ons:
-
Cell Hashing / CellPlex multiplexing
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
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
We:
-
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
