Single Cell Genomics
Single Cell Genomics
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
10X 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% (NextGEM)
Capture 1,000 - 20,000 cells with capture rate of ~70-80% (GEM-X)
- 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: CITE/Hashing/other library preparations
*Contact us for more information about our preferred vendors for antibodies.
Newly Released Products from 10X Now Available!
GEM-X:
- Higher Throughput (up to 20,000 cells versus 10,000 for NextGEM)
- Increased Sensitivity (two-fold increase in detected genes, detection of rare transcripts)
- Improved Recovery (Highly viable cells can have a capture rate of up to 80%)
*Please note: NextGEM is being discontinued at the end of 2025 and we will move all projects to GEM-X reagents.
FLEX:
- Profile gene expression for thousands to hundreds of thousands of cells or nuclei with a sensitive probe based method that captures the whole human or mouse transcriptome to detect even low-expressing genes
- Store samples without losing data quality, allowing you to batch samples in the same run and minimize experimental variability
- Fix fresh samples at collection to lock in biological states and preserve fragile cells
- Reduce experimental variability and increase efficiency by batching and multiplexing samples
- Probe-based method for human and mouse. Custom probe options available
- Visit the 10X site about FLEX to learn more.
On-Chip Multiplexing:
- No barcoding prior to capture like with Hashing - reduce time and loss with tagging prior to capture
- Sample multiplexing is accomplished by partitioning up to four samples from each multiplexing set with corresponding gel beads (each containing a unique list of barcodes). A pool of GEMs is generated in a single recovery well for each set. The GEM pool in each recovery well is used to generate cDNA, where DNA derived from a cell shares a common barcode.
- Visit the 10X site about On-Chip Multiplexing to learn more.
Each sample can have up to 5,000 cells for a total of 20,000 cells per capture (or group of 4)
4 samples must be included
For more information about single cell experiment project design or to schedule a 10X capture, please contact us.
Additional testing underway by GRC staff to evaluate other methods such as Illumina Single Cell 3' RNAseq and Parse Biosciences. Contact us to learn more!
Plate-based Methods
Smart-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.