Shared Resource Spotlight: Single Cell Analysis

The Single Cell Analysis shared resource provides researchers with experimental and comprehensive computational support for single-cell RNA-Sequencing (scRNA-Seq) and single-cell ATAC-Sequencing (scATAC-Seq). The group is led by faculty director, Peter Sims, PhD, and director, Erin Bush, and operates within the Columbia Genome Center and the Herbert Irving Comprehensive Cancer Center.

Large-scale single-cell RNA sequencing has made it possible for scientists to analyze tens of thousands of cells while simultaneously obtaining imaging and genomic data from each individual cell. The SCA shared resource provides end-to-end project support for single-cell sequencing experiments, including project design and experiment planning. The group also offers equipment for self-use at no charge for cell or tissue dissociation, and flexible scheduling for transportation of cells. The SCA core performs the entire experiment, from library preparation to sequencing at the Genome Center to analytics.

Given that single-cell RNA-seq presents numerous analytical challenges, and that computational techniques in this area are rapidly evolving, the SCA shared resource provides bioinformatics support for processing, quality control, analysis, and interpretation of data generated as an additional service. More information about this service can be found here.

Additionally, to serve researchers with smaller experiments, the SCA group offers an in-house developed single-cell method for sorting in 96-well plates. This option works nicely for pilots or for rare cells or subtypes, and the SCA team works closely with flow shared resources on campus to optimize this workflow.

The SCA group is working also to update their analytics pipeline to make it faster and more scalable for users.