Single Cell Technology Core Services

Let us help you design your next experiment! A well-controlled and balanced study will maximize information and minimize the overall cost. We offer consultations to help you decide the best platform and analysis strategy. Schedule a meeting with core director Dr. Mei Zhang, zhangm5@chop.edu, to learn about all services and technologies available.

Supported Assays

• Single Cell Gene Expression (3′ GEX)
• Single Cell Immune Profiling (VDJ and 5′ GEX)
• Single Cell Assay for Transposase Accessible Chromatin (ATAC)
• Single Cell Multiome (3'GEX + ATAC)
• Single Cell Fixed RNA Profiling

Sample Requirements

Clean single cell or nuclei suspension free of debris and clumping
Cell Viability: >90% ideally, >70% is acceptable
Cell/nuclei concentration:700-1200 cells/ul

Preferred Buffers
1X PBS (calcium and magnesium free) containing 0.04% weight/volume BSA (400 μg/ml).

PBS can be replaced with most common cell culture buffers and media if necessary.
Media should not contain excessive amounts of EDTA (> 0.1mM) or magnesium (> 3mM), as those components will inhibit the reverse transcription reaction.
Any surfactants (Tween-20, etc.) should also be avoided as they may interfere with GEM generation.

For nuclei: include 0.2U/μl RNase Inhibitor (Sigma Protector RNase inhibitor, PN-3335399001 is strongly recommended) in the buffer for gene expression or multiome (gene expression + ATAC) studies.

NanoString's GeoMx Digital Spatial Profiler (DSP)

Supported assays

• GeoMx Human Whole Transcriptome Atlas: 18,000+ human protein-coding genes
• GeoMx Mouse Whole Transcriptome Atlas: 20,000+ mouse protein-coding genes
• GeoMx Cancer Transcriptome Atlas: 1,800 human genes

Sample Requirements

• Compatible samples: FFPE, Fresh or Fixed Frozen tissue
• For best results, do not use FFPE blocks that are greater than 10 years old
• It is essential to minimize RNases when processing fresh frozen tissues
• Fisherbrand SuperFrost Plus slides or Leica BOND plus slides
• Sectioning: FFPE 5 μm; Frozen 5-10 μm
• Scan area (green area in the picture): 35.3mm x 14.1mm
• Multiple sections can be mounted on the same slide, at least 2-3 mm apart

Vizgen MERSCOPE

Supported assays:

Custom designed gene panels for 140, 300, or 500 genes

Sample Requirements

• Compatible samples: FFPE, Fresh or Fixed Frozen tissue
• Maximum size: 1cm³
• Sectioning: FFPE 4 or 5 μm; Frozen 10 μm
• Mounted on MERSCOPE slides
• RNA quality:
• Frozen tissue: RIN>7 ideal; RIN 5-7: detection efficiency diminishes; RIN<5: do not proceed
• FFPE: DV200>60% yield high quality data; DV200 40-60% yield quality data; DV200<40% yield low quality data

We strongly recommend testing sample quality with the MERSCOPE Sample Verification Kit.

NanoString's GeoMx Digital Spatial Profiler (DSP)

Supported assays

• GeoMx protein assays for nCounter
• GeoMx protein assays for NGS

Sample Requirements

• FFPE, Fresh or Fixed Frozen tissues
• For best results, do not use FFPE blocks that are greater than 10 years old
• Fisherbrand SuperFrost™ Plus slides or Apex BOND® slides
• Sectioning: FFPE 5 μm; Frozen 5-10 μm
• Tissue sections need to be mounted within the scan area (green area in the picture): 35.3mm x 14.1mm
• Multiple sections can be mounted on the same slide, at least 2-3 mm apart

Akoya Phenocycler

Supported assays

• Akoya inventoried antibodies for human fresh frozen and FFPE, and mouse fresh frozen
• Custom conjugated antibodies

Sample Requirements

• FFPE, Fresh or Fixed Frozen tissues
• Coverslips (22mm x 22 mm, Akoyabio) coated with poly-L-lysine
• Tissue sectioning: 5-10 μm (FFPE 4-5 μm, Frozen 8-10 μm); up to 15mm x 15mm

Our experienced bioinformaticians help with experimental design, developing reproducible workflows, analyzing high throughput next-generation sequencing data and spatial profiling data, and supporting manuscript development/publication. We generate visualizations of complex data and assist data uploads to public repositories.