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10x Genomics Single Cell Services:
  • FACS
  • Single cell library preparation (RNA-Seq, ATAC-Seq, etc…)
  • Sequencing and basic data processing

The Advanced Analytics Core now offers turnkey 10x Genomics single cell services. Simply provide a single cell suspension, and the Core will perform the services necessary to generate high quality sequencing data: cell sorting, library preparation, sequencing, and basic data analysis.

The 10x Genomics Chromium System encapsulates hundreds to tens of thousands of cells (or nuclei) into uniquely addressable partitions in minutes, each containing an identifying barcode for downstream analysis. Up to eight samples can be processed simultaneously, and multiple runs can be conducted in a single day. Encapsulation is not biased by size and is compatible with fresh, frozen, and methanol-fixed samples. Applications of the Chromium System include:

  • Gene expression profiling
  • Immune profiling
  • CRISPR screening
  • Copy number variation
  • Chromatin accessibility (ATAC-Seq)
  • Cell surface protein characterization (CITE-Seq/REAP-Seq)

GemCode Technology provides a precisely engineered reagent delivery method that enables thousands of micro-reactions in parallel. Gel beads infused with millions of barcoded oligonucleotides are mixed with a sample and then added to an oil-surfactant solution to create gel beads in emulsion (GEMs). Barcoded products are pooled for downstream reactions to create short-read sequencer compatible libraries. After sequencing, the resulting barcoded sequences are fed into analysis pipelines that use the barcode information to map reads back to their original cell.


10x Genomics Chromium Single Cell Controller


FACS: Sample preparation via FACS can be completed by the Core. Contact the Associate Director to arrange a consultation.

Single-Cell Isolation & 10x Library Preparation: Each 10x chip is comprised of eight sample inlets into which single cell suspensions are loaded. Each inlet can encapsulate as many as 10,000 cells or as few as 500 cells. Multiple chips can be run on a single day. The Core recommends providing at least 50,000 cells in suspension per sample, as fewer cells can make important QC steps difficult to accomplish.

Sequencing & Basic Data Processing: Libraries are sequenced on the NextSeq 500 sequencing system. High-output sequencing kits produce ~400M read pairs, covering up to 20,000 single cell gene expression libraries at the suggested minimum depth of 20,000 read pairs/cell. The more economical mid-output kits (130M read pairs) may be appropriate when working with low abundance samples or specialized applications (e.g. immune profiling). The NovaSeq, available through UNC’s High-Throughput Sequencing Facility (HTSF), may be used for very large scale projects or for those which require additional read depth.

For our standard 3’ or 5’ gene expression service, the end user will receive raw read counts as well as pre-analyzed data which can be viewed on 10x’s Loupe Cell Browser. The Loupe Cell Browser allows investigators to easily gain insights into their data without writing a single line of code. Applications include finding significant genes, identifying cell types, exploring substructure, integrating gene expression and V(D)J analysis, and sharing results. To see some of these features for yourself, try out 10x’s Loupe Cell Browser Gene Expression Tutorial.

Other 10x protocols will include different deliverables. Please contact the Associate Director for more information.

How to start a project:

To begin a project using the 10x system, please contact the Associate Director to arrange a consultation with the Core Director, Dr. Scott Magness. Dr. Magness will review experimental goals with the investigators and provide advice on experimental design to ensure the needs of the end-user are met. The AA Core will then schedule the project, coordinate with the end-user for cell drop off, and discuss pricing and turnaround estimates for project completion.

Pricing estimates:

10x Single Cell 3’ or 5’ Library Preparation

Number of 10x Samples Price per Sample* UNC/NCSU/CGIBD Member Price**
First Sample ~$3,269.74 ~$2,870
Samples 2 through 8 ~$2,086.62 ~$2,020


10x ATAC Library Preparation

Number of 10x Samples Price per Sample* UNC/NCSU/CGIBD Member Price**
First Sample ~$2,346.50 ~$2,080
Samples 2 through 8 ~$1,693.31 ~$1,660

* Price estimate for standard service including chip, reagents, and assay service.

** Investigators affiliated with UNC, NCSU, or the CGIBD receive discounted pricing.


Pricing for other 10x single cell services is available upon request: Immune profiling, CRISPR screening, copy number variation, cell surface protein characterization (CITE-Seq/REAP-Seq). Please contact the Associate Director for a personalized quote.

10x Sequencing & Basic Data Processing
Sequencing Kit Price per Run* UNC/NCSU/CGIBD Member Price**
NextSeq Mid-Output 150 cycles ~$1,446.02 ~$1,310
NextSeq Mid-Output 300 cycles ~$2,239.87 ~$2,040
NextSeq High-Output 150 cycles ~$3,609.81 ~$3,310
NextSeq High-Output 300 cycles ~$5,866.92 ~$5,085

* Price estimate for standard service including materials, labor, and basic data processing.

** Investigators affiliated with UNC, NCSU, or the CGIBD receive discounted pricing.

Submitting Samples:

Users may schedule an appointment to drop off samples in the AA Core single cell laboratory:

AA Core MBRB Laboratory

Medical Biomolecular Research Building (MBRB)

Room 4331

111 Mason Farm Rd

Chapel Hill, NC 27599