Core Facilities

Single Cell Immunophenotyping Core

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

Our SCIC offers cutting-edge NGS and QC devices, providing significant advantages to core users. Firstly, users have unrestricted access to these devices, enabling their utilization 24/7, on any day, including weekends, holidays, and even during summer and Christmas. Secondly, the core ensures rapid data delivery, guaranteeing that users receive their results on the same day as their runs. Lastly, by utilizing the NGS devices, users gain invaluable skills, fostering their career development and enhancing their prospects for securing better job opportunities post-graduation.

Next-Generation Sequencing: The core operates two Illumina and one Nanopore sequencer respectively: NextSeq 2000MiSeqP2 Solo and MinION M1K. 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. After receiving training, users are free to reserve the instruments and run their experiments independently.

Announcement:

to be continued.

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: +B%$1eL2

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

Topic:

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.

Agenda:

  • 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

Single Cell Immunophenotyping Core Seminar Series: Working with Sequencing Data: From Flow Cell to Single-Cell 

Speaker: Jonathan MATTHEWS | Tay Lab, SCIC User; MEng, Electrical Engineering and Computer Science (BioEECS), MIT, 2016; BS, Electrical Eng. & Computer Sc., MIT, 2015



When: Wednesday, May 17, 2023

What time: 12:00 PM CT – 1:00 PM CT

Where: Zoom

Topics:

Join us for an informative seminar on the efficient handling of sequencing data in the RCC's flagship HPC clusters, Midway2 and Midway3, housed in the University of Chicago's data center. Our community benefits from state-of-the-art computing infrastructure that provides ample computing power and fast internet speed for enabling discovery and innovation.

The seminar will cover the following topics:

  • Monitoring sequencing runs in BaseSpace using examples of good and bad quality check scores.
  • Transferring BaseSpace Sequence Hub data, including Binary Base Call (BCL) and FASTQ files, to the RCC through Midway2 or Midway3 using the command line interface (CLI).
  • Requeuing BCL files using the BaseSpace BCL Convert App.
  • Uploading sequencing data from the RCC to the 10X Genomics Platform for processing using the Cell Ranger App.

Join us for this informative seminar to learn how to efficiently handle sequencing data in order to generate meaningful knowledge for scientific purposes.

Presentation File

 

Single Cell Immunophenotyping Core Seminar Series: Nanopore Applications: Next Generation Sequencing with NanoPore

Speaker: Dr. Filip Boskovic | Szostak Lab, SCIC User; HHMI Postdoctoral Associate and EMBO Postdoctoral Fellow, UChicago, HHMI; PhD, University of Cambridge, 2022

Dr Filip

When: Tuesday, September 19, 2023

What time: 12:00 PM CT – 1:00 PM CT

Where: Zoom

Topics:

Join us for an informative seminar on the efficient handling of sequencing data in the RCC's flagship HPC clusters, Midway2 and Midway3, housed in the University of Chicago's data center. Our community benefits from state-of-the-art computing infrastructure that provides ample computing power and fast internet speed for enabling discovery and innovation.

The seminar covers the following topics:

  • An Expedition through Nanopore Sequencing Advancements
  • A Comparative Dive into Sequencing Technologies
  • Masterful Tips and Tricks for Successful Nanopore Experiments
  • Guided Tour of the General Sequencing Pipeline
  • Unveiling Enhanced Data Analysis Techniques
  • Accessible Links and Resources for Aspiring Nanopore Adventurers.
  • Q&A (15 min.)

Join Us for an Informative Webinar on Nanopore Sequencing Technology. Discover the potential of Nanopore sequencing and its applications in modern genomics research.

Whether you're new to technology or looking to enhance your skills, this webinar is for you.

10x Genomics summarized their spatial omics tools and noval upgrades such as Visium-HD. You will learn how Chromium Single Cell, Visium Spatial, and Xenium In Situ platforms from 10x Genomics can help you push the boundaries of your research. Uncover molecular insights, dissect cell-type differences, investigate the adaptive immune system, detect novel subtypes and biomarkers, and map the epigenetic landscape cell by cell. Enabling deeper insight into cancer, immunology, neuroscience, and developmental biology, 10x Genomics gives researchers the ability to see biology in new ways.

  • Speakers: Egon Ranghini (email, LinkedIn) from 10X Genomics, Michael Andrade from UChicago Medicine (email, LinkedIn), and Leilani Marty Sentos.
  • Organizers: Fatih Abasiyanik (abasiyanik@uchicago.edu) and Heather Eckart (heather.edkart@10cgenomics.com)
  • Location: Eckhardt building, ERC 301B.
  • Date & Time: Wednesday, January 10, 2024; 14:00-15:30

Video Link and Passcode: r^5i*KQ

 

This is a special hybrid seminar organized jointly by the Single Cell Immunophenotyping Core and Illumina!

The seminar will focus on introducing the XLEAP-SBS™ Chemistry on the NextSeq™ 2000 and the NovaSeq™ X Plus instruments.

Seminar Details:

  • Date: 15th May, 2024
  • Time: 10:00-11:30
  • Location: William Eckhardt Research Center, Room 201B
  • Topic: Introducing XLEAP-SBS™ Chemistry on the NextSeq™ 2000 and the NovaSeq™ X Plus
  • Speakers: Logan Silber (Sequence Sales Specialist) and Chevelle Blackburne (FAS)Dr Filip

Event Objectives:

  • Understand the features and benefits of XLEAP-SBS™ Chemistry
  • Explore the enhanced performance of the NextSeq™ 2000 and NovaSeq™ X Plus instruments
  • Gain insights into designing experiments to leverage the latest advancements in sequencing technology

Seminar Details:

Title: Spatial Protein Phenotyping with Phenocycler-Fusion Technology

Date: May 29, 2024, 11:00 AM -12:00 PM; Location: ERC 201 B

Speaker Lineup:

  • Avik Mukherjee, PhD, Sr. Technical Applications Scientist, Akoya Biosciences

  • Surya Pandey, PhD, Northwestern University Immunotherapy Assessment Core

Characterizing the complexities of the tissue microenvironment is critical in understanding the molecular and cellular mechanisms driving disease and therapeutic response. Protein spatial phenotyping enables the determination of which cells are present, their location, their biomarker patterns, and how they are organized and interact with each other. The PhenoCycler-Fusion™ (formerly CODEX®) technology provides a comprehensive solution for whole-slide, single-cell, spatially resolved, multiplexed immunofluorescence, allowing quantitation and spatial visualization of 80+ protein markers. This high-throughput format complements spatial transcriptomics data and can significantly advance your research.

Calendar, Flyer 

 

Standard Operating Procedures