Core Facilities

Single Cell Immunophenotyping Core

The Single Cell Immunophenotyping Core Facility is a fully user self-service facility that provides access to specialized instrumentation for phenotyping and genotyping of immune cells. These include flow cytometry and single-cell next-generation sequencing technologies. All instruments are located in the laboratories of four different CIIC investigators (ERC 318 and KCBD 10220E), and are available for use by the larger UChicago community.

Flow Cytometry. The BSD's Cytometry & Antibody Technology Core Facility manages two flow cytometers in ERC 318 for the core. For more information on these two instruments, click here.

Next-Generation Sequencing. The core operates two Illumina sequencers - the NextSeq 550 and the MiSeq. After receiving training from our personnel, users are free to reserve the instruments and run their experiments independently. The core has a service agreement with Illumina that covers reagent replacement if a machine error causes the researcher to lose their sample and disposables.

Single Cell Library Preparation. The core operates a 10X Genomics Chromium Controller, which is the key enabling technology for single cell sequencing applications. Due to the highly technical requirements of this machine, usage of the instrument requires core personnel supervision. In addition, quality control of DNA/RNA preps and libraries is accomplished via the Agilent TapeStation 4200. We will eventually provide links here to reagents/disposables that you will have to provide in order to use this machine.

qPCR. The core operates a BioRad CFX384 qPCR system to enable real-time quantitative PCR in 384-well plate formats. For standard 96-well plate qPCRs, we also have access to a Roche Lightcycler 96 that we can share with users (free at the moment). After receiving training, users are free to reserve the instruments and run their experiments independently.






Our core partnered with 10x Genomics to offer a hybrid Lunch & Learn event on April 27, 2022. This was an exciting opportunity to learn about 10x Genomics' current and upcoming single cell technologies, how to process samples at the Core, and see how single cell resolution can add depth to research questions. The speakers were Egon Ranghini (email, LinkedIn) from 10X Genomics, Michael Andrade from UChicago Medicine (email, LinkedIn), and our the Core Manager, Ha-Na Shim. Location: Eckhardt building, ERC 301B.

Please see the attached presentation and video link. PassCode

A Scientific Seminar: Unifying Workflows: From Sample to Data

When: Wednesday, July 13, 2022

What time: 11:00 AM CT – 1:00 PM CT

Where: 1103, KCBD

Single-cell analysis is a powerful technique to characterize complex tissue types, identify rare cell populations, uncover regulatory relationships between genes, and track cell trajectories. From sample handling to cell dissociation, there are a number of technical considerations that influence cell viability and data quality of single-cell genomics, single-cell epigenomics, and single-cell gene expression experiments.

Join us for this seminar, which covers critical sample prep decisions and technical considerations for single-cell assay design and optimization.


  • 11:00am - 11:45am: General Sample Preparation Overview and Core Introductions
  • 11:45am - 12:30pm: Breakout sessions 1-3
  • 12:30pm - 1:00pm: Social and Group lunch

Breakout Sessions: Attendees split into 3 cohorts and will visit each Breakout session
• Organoids/Pathology (Le Shen and Chris Weber-Core)
• FACS (David Leclerc-Core and Miltenyi)
• Single Cell (Ha-Na Shim, Fatih Abasiyanik, Pieter Faber-Cores, and 10x Genomics)

The flyer and its power point presentation

Standard Operating Procedures