Single Cell

The High-Throughput Genomics and Bioinformatics Shared Resource offers end-to-end service in a growing list of single cell genomic applications supported by 10x Genomics. Our analysis services are highly customizable to the unique requirements of your single cell experiment. To date we have supported single cell studies profiling gene expression, immune V(D)J clonotypes, and chromatin accessibility. We also suppport emerging single cell applications upon demand. 

Getting Started

Online Resources

The tab 'Education & Resources' on 10x Genomics website provides links to diverse training materials for single cell profiling applications. In particular, 10x University is a convenient environment to learn about the technology and train your skills in generating/analyzing single cell data. If you have specific questions, it may have been addressed on the searchable Q&A knowledge base. For general technical knowledge, see their support section

Contact a single cell expert

Please contact Brian Lohman in the Bionformatics Shared Resource to discuss analysis options by sending an email to bioinformaticshelp@bio.hci.utah.edu.  If you need help with sample preparation, check the FAQ from the High-Throughput Genomics Shared Resource.

Analysis

Turn-Key

10x Genomics' Cell Ranger software contains robust bioinformatics pipelines that transform raw sequencing data into a browsable format that requires little bioinformatics experience. Cell Ranger has a turn-key analysis in place for gene expression, which automatically maps reads to the genome, performs QC, distinguishes cells against background noise, clusters cells, renders t-SNE visualizations, and reports differential expression. If the turn-key analysis from Cell Ranger is not sufficient, contact us for a customized analysis.

Custom

Special analysis may be required for a number of reasons, including but not limited to the following examples:

  • Multi-species contamination (e.g. PDX samples)
  • Experiment design models a differentiation process that requires a trajectory analysis
  • Automatic analysis has cluster misspecification
  • Incorrectly distinguished cells vs. background
  • Building a custom genomic reference

This is a rapidly changing field with new methods emerging often. If you don't see what you are looking for, we will help apply your favorite new tool. Please consult this actively curated database of scRNA tools for finding the right solution.

Contact Us

Bioinformatic Analysis Director
David Nix, PhD
david.nix@hci.utah.edu
801-587-4611

Bioinformatic Analysis Associate Director
Timothy Parnell, PhD
timothy.parnell@hci.utah.edu
801-587-4312

Governance

HCI Senior Director Oversight
Alana Welm, PhD

Faculty Advisory Committee Chair
Katherine Varley, PhD

Faculty Advisory Committee Members
Richard Clark, PhD
Jason Gertz, PhD
Christopher Gregg, PhD
Philip Moos, PhD
Sean Tavtigian, PhD
Katherine Varley, PhD
Joseph Yost, PhD