The GRCF is excited to offer genomic applications for single cells

We offer end-to-end,   full service single cell capture, library preparation and high throughput sequencing utilizing technologies offered by 10x Genomics. Methods are available for 3′, 5′, VDJ enrichment, and ATACseq protocols, each targeting up to 10,000 cells or nuclei/sample.  Single-cell libraries can be sequenced directly through the GRCF on the Illumina NovaSeq X plus, Illumina’s most high throughput sequencer providing the lowest cost per base.

An Overview of the Technology

High-throughput molecular barcoding

Cell-by-Cell 3’ or 5′ end counting of mRNA transcripts

Tens of thousands of cells per run, simultaneous runs possible

Consultation on cell preparation prior to capture


What Is The Chromium X?

Chromium X is 10x Genomics most flexible and newest instrument. It runs all single cell assays, including new high-throughput assays for Single Cell Immune Profiling and Single Cell Gene Expression. The Chromium X is compatible with all 10x Genomic current single cell assays, including low-, standard- and high-throughput options. The Chromium Controller (available for self-service) runs low- and standard-throughput assays. 

What Does End-To-End Service Through The GRCF Mean?

 After consultation with our Single Genomics team, customers can drop off a single cell suspension of cells they would like captured. We work to establish an agreed upon capture rate, perform the capture, sequencing libraries, quality libraries are sequenced and data returned after first pass analysis on the open source, 10x pipeline Cell Ranger.  Our goal is to make the process from cells to usable data as seamless as possible to the researcher.

Should I Use Single Cells Or Nuclei For My Experiment?

Cells that are too large for the microfluidics channels of the 10x Chromium system, present a challenging shape or are not easily dissociated from tissue, would be more suitable for nuclei isolation.

What Do I Need To Consider in Preparing Cells?

Single cell capture works most effectively when cells are less than 30 microns in size, cells are fully dissociated and in a single cell suspension, minimal debris is present in the suspension and cells present with greater than 90% viability. 

The cell processing efficiency in capture is 65%. Cell capture targets can range from 500- 10,000 cells. A minimum of 2.5 x the target cells will be needed to ensure a successful capture.

What makes a good quality single cell sample?


Single cell suspensions must be free from debris, cell aggregates, and any other contaminants (such as background RNA, DNA, or EDTA).


You want your cells to be alive! We recommend at least 90% viability.


Unless you are using isolated nuclei, it’s very important to maintain intact cellular membranes, which requires that the cells be treated very gently. We recommend using wide-bore pipette tips to slowly, gently resuspend cells.

10x Genomics Chromium X System

 This technology supports a broad range of applications, including cancer-cell transcriptomics and cell-type identification and discovery. Because the platform works with short read sequencers, it integrates easily into the existing GRCF RNAseq workflow.

Reserve Time on the Chromium System

The GRCF is currently offering ‘self-service’ and training opportunities on the 10x Genomics Chromium system. The well-characterized pipeline and unique software, allows the GRCF to offer analysis for 10X Genomics data. The GRCF  cost for sequencing will vary based on read length.

Our pricing list for the most frequent requests

3′ or 5′ Capture &  Library Preparations

$ 3,000
First Sample

Capture up to 10,000 cells

  • Discounts for multiple specimens
  • Access to Cell Ranger software
  • Samples 2-8= $2800/ capture (8 samples per chip)
  • Secured scheduling
  • Fast turnaround times
  • First pass analysis

3′ or 5′ Capture & Library Preparations using Chromium HT

$ 6,000
First Sample

Capture up to 20,000 cells

  • Discounts for multiple specimens
  • Access to Cell Ranger software
  • Samples 2-8 = $2800/ capture; 9-17= $2000/capture
  • Secured scheduling
  • Fast turnaround times
  • First pass analysis
$ 2,400 $ 1,400
per lane

~2.5 Billion Paired Reads

  • Opportunities for economies of scale
  • Possible pooling of libraries to a single lane
  • Fast turnaround times
  • First-pass data analysis included
  • Seamless end-to end services
  • Heavily quality controlled processes
  • Please contact us to discuss your unique project needs. These prices are meant to offer a ballpark-estimations and may not be comprehensive to your unique experiment. 
  • Our center offers additional single cell support services such as VDJ enrichment, ATAC seq, nuclei isolation etc. Please reach out to discuss your needs.

Single Cell Genomics through the GRCF is a joint effort between the Cell Center & DNA Services

We offer support on single cell isolation, training for capture and sequencing and analysis service.

Contact us today for more information or to schedule for your experiment.