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URMC / Research / Rochester Genomics Center / Services / Single Cell & Spatial Genomics
 

Single Cell & Spatial Genomics

Marlene Balys performing a single cell experiment in the lab

Why Choose Single Cell?

The Genomics Research Center is always researching and finding new methods for single cell research. The following platforms are currently available at the GRC. 

10X Genomics

10X10X Chromium Controller
The 10X Chromium system is a droplet based system capable of capturing up to 10,000 cells per capture. 
Current Capabilities of this platform:
1. Single Cell Gene Expression Profiling
2. Single Cell Immune Profiling
3. Single Cell CNV
4. Single Cell ATAC​

Learn more about the 10X Chromium System

10X Capture Sample Preparation Considerations:
- Capture 1,000 - 10,000 cells with capture rate of ~65%
- Flow sort prior to capture, if possible (isolate particular cell types, remove dead cells)
- Bring GRC single cell suspension with viability >70%

Cell Hashing, CITEseq, and Feature Barcoding Options:
Options available for multiplexing to lower capture costs and increase cluster identification: 

- Cell Hashing: Oligo-tagged antibodies* bind ubiquitously expressed surface proteins allow for unique labeling of samples that can be pooled for a single 10X capture
- CITEseq: Cellular Indexing of Transcriptomes and Epitopes by Sequencing. Antibody* bound oligos act as synthetic transcripts for detection of proteins in quantitative readout. 
- Feature Barcoding: 10X version of CITEseq - cell surface protein expression and gene expression from same cell. 
*Contact us for more information about our preferred vendors for antibodies. 

For more information about single cell experiment project design or to schedule a 10X capture, please contact us

Fluidigm

FluidigmC1Fluidigm C1

Isolate up to 800 individual cells and examine for viability, surface markers, or reporter genes. Flexible options for mRNA sequencing, DNA sequencing, epigenetics and miRNA expression. Focus on cell diversity, tissue heterogeneity, gene specific expression, isoform expression, epigenetic analysis, and genomic variants. 

Learn more about the Fluidigm C1 System

Mission Bio

MissionBioTapestriMission Bio Tapestri

Targeted Single-Cell DNA Panels with catalog and customizable content. 

Hematologic Malignancies
Solid Tumor Profiling
Genome Editing

Learn more about the Tapestri Platform

BD Rhapsody

RhapsodyBD Rhapsody Single Cell System

Capture and index single cells using magnetic beads. Analyze gene expression of thousands of cells using predesigned or customized assays. Downstream analysis using Rhapsody system analysis software. 

Learn more about the BD Rhapsody Platform

Plate-based Methods

SmartSeq2 protocol imageSmart-seq 2
An example of a plate based method is Smart-seq2. In this approach, single cells are placed into each well of a 96-well plate through flow sorting or micro capillary pipetting. With this approach, full length transcripts are captured which allows for detection of splice variants and investigation of SNPs. This method still utilizes the capture of poly(A) RNA and does not indicate strand orientation. Please contact us for more information about this single cell approach. 

 

Spatial Genomics

10X Visium Spatial Gene Expression

Measure gene expression activity in the context of tissue microenvironment.

Visium with H&E: Use H&E staining for morphological context: 
Spatial_Mouse

 Visium with IF: Combine Gene expression with Immunofluorescent staining for Spatial Proteomics:



Gene expression slides contain 4 capture areas that each contain 5000 barcoded spots. Each spot contains oligonucleotides with spatially barcoded sequences revealing the location of the mRNA transcripts in the tissue.

Learn more about 10X Visium Spatial Gene Expression.

Contact us for information about the technology including tissue optimization and setting up a spatial gene expression study.