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.
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External Links
Key Services:
10X Genomics Visium Spatial Transciptomics
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Spatially resolved whole-transcriptome analysis
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6.5 x 6.5 mm or 11 x 11 mm formats
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Starting Matrials:
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Fresh Frozen OCT embedded tissue
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FFPE blocks
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Hard-mount FFPE, H&E-stained slides
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Two resolutions:
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SD - Spot width 55um, center-to-center distance 100um
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HD - 2 um grid binned into 2um, 8um or 16 um bins
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10X Genomics Xenium Spatial Transciptomics
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Spatially resolved transcriptome data @ subcellular resolution
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300-500 and 5000 gene panels
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2 slides per run, 1cm x 2cm imageable area each
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Start from Fresh Frozen OCT or FFPE blocks
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Premade + add-on and fully custom gene panels
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Panel design assistance service
10X Genomics Single Cell Flex (Fixed RNA Profiling)
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Up to 128,000 cells per lane across up to 16 samples
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Probe-based RNA profiling
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Batch together samples collected and fixed at different times or from FFPE tissue blocks.
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Lowest cost per sample
10X Genomics Single Cell 3’ Gene Expression
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2,000-20,000 cells per lane
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Oligo-d(T) primed, 3'-biased digital gene expression
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Best option for pure expression profiling
Add-ons:
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Cell Hashing / CellPlex multiplexing
10X Genomics Single Cell 5' Gene Expression
Enables Single Cell Immune Profiling:
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Paired TCR alpha- and beta chain V(DJ) sequencing
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Paired BCR heavy and light chain V(DJ) sequencing
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Combined Immune Profiling 5’-Gene Expression
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BEAM: (Bar-Enabled) Antigen Mapping
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Identify B- or T-cell clones binding to a labeled antigen
10X Genomics Single Cell ATAC-seq
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Genome-wide Chromatin Accessibility in single cells
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2,000-8,000 cells per lane
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Promoter / enhancer accessibility
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Motif enrichment / discovery
10X Genomics Multiome ATAC + Gene Expression
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2,000-8,000 cells per lane
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Paired 3’ nuclear gene expression and chromatin accessibility from single cells
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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:
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15 ul of purified RNA at 25 ng/ul or more per sample
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96 well plate of cells frozen in lysis buffer
We:​
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Perform Well-Barcoded RT reaction + cDNA pooling
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Sequence using the Illumina NextSeq platform
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Deliver FASTQs, BAM files, gene counts matrix
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Frozen Nuc-Seq
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Fresh or flash-frozen tissue
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On-site FACS sorting & direct-to-10X workflow
