Skip to main content

Saturday, July 20:  All UR Medicine facilities are open as scheduled and providing safe patient care, with a goal to return all clinical services to full efficiency by early next week.
Patients: click here for more information. Faculty/Staff: click here for information.

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

Single Cell 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%

10X releases 3' CellPlex:
10X Workflow for 3' CellPlex

Pool up to 12 samples and capture as many as 30,000 cells per channel. Learn more about the 3' CellPlex from 10X Genomics

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

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.