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Indiana University School of Medicine
Indiana University School of Medicine
Service Cores

Single Cell Studies

The Center for Medical Genomics uses 10x Genomics Chromium Systems for single-cell analysis. The 10x system is a droplet-based scRNA-seq platform that allows genome-wide expression profiling for up to 10,000 cells at once. Using a 12-base molecular barcoding system, the unique molecular identifier (UMI) is used to directly quantify the expression level of each gene in each cell.

In addition, the center supports library preparation from the cDNA generated using microfluidic-based systems such as C1 Fluidigm systems.

Single-Cell Analysis Services

The following services are supported using the 10x Genomics Chromium system:

  • single-cell or single nucleus RNA-seq
  • single-cell ATAC-seq
  • single-cell CNV (Copy Number Variation)
  • single-cell immune profiling (with antigen specificity and cell surface proteins)
  • CITE-seq

Before each single-cell experiment, the center requests a project planning meeting including the PI, experimentalists (lab technician, postdocs or graduate students), core staff, and bioinformatician. In this meeting, the key experiment logistics are discussed, including cell quality assessment, experiment scheduling, expectation, analysis plan and data dissemination. The center also encourages a “dry run” before an experiment to assess the quality and quantity of the single-cell suspension. 

View the checklist for single cell experiments

Request a Meeting

To schedule a meeting to initiate a Single-Cell Analyses Service, contact the center’s program manager.

Single Cell Studies FAQs

The center has successfully generated single-nucleus RNA-seq and ATAC-seq from the nuclei isolated from the post mortem fresh-frozen brain samples. However, users are expected to isolate their nuclei. Normally, much fewer genes will be identified from the nuclei isolation compared to the cell suspensions.