Core Facilities

SCIC User Policies

The Single Cell Immunophenotyping Core Facility is a user core facility that seeks to provide training on next-generation sequencing technologies for single cell applications. As a user facility, this means that researchers can expect to receive training and orientation to the lab and its instruments, and then eventually the ability to reserve the instruments for independent data collection and generation.

We highlight that similar capabilities for specimen processing and data generation are available in the form of a service facility through the UChicago Genomics Facility managed by Dr. Pieter Faber. As such, if you envision needing to perform a next-generation sequencing study in one-off fashion (i.e.: non-routine study), we highly recommend users to contact the Genomics Facility first.

On the other hand, if you do envision needing to run next-generation sequencing studies as a routine procedure for your projects, then it would justify the level of training and specialized hands-on technical experience that you should expect to invest before embarking on your first study with us. If this is you, read on, and make sure to bookmark our website for the latest updates and information on the core.



It is our goal to provide all core facility users with access to state-of-the-art instrumentation and as seamless of an experience as possible, from training to reservations to billing. In engaging with the core facility and its instruments, we hope all users can abide by the following general rules in order to help us in our mission for other users as well.

All users must:

  • Complete and update your training and familiarity with the UChicago chemical hygiene plan and fire safety policies.
  • Be properly trained for all instruments that they seek to use.
  • Reserve all instruments ahead of usage.
  • If a reservation is not needed anymore, cancel reservations ahead of time or by emailing core staff.
  • Access the instruments only within your reservation time, and be aware of which users may come after you to notify them if there are any issues or if your experiment may run longer than expected.
  • Use instruments according to posted standard operating procedures (SOPs) for their preparation, usage, and cleaning. This is imperative to ensure that the instruments are ready for the next user.
  • Sign out by logging your instrument usage on the paper-based log forms next to the instruments.
  • Transfer and back up your data. Absolutely no thumb/flash drives and portable hard drives allowed with the instruments.
  • Notify core staff if and when any issues arise, however minor. Seemingly minor issues might actually be signs of more serious problems.
  • Maintain the cleanliness of the workspaces.
  • Keep updated with status messages and updates from the core staff.



A new user is defined as a researcher who has not previously engaged with the core facility. Our process for onboarding new users includes the following steps:

  • Internal Users: You must complete the user registration, including providing billing contacts for your department or better yet, a FAS code for your project.
  • External Users: Even if you’re a consortium (Northwestern/UIC) user, please contact core staff to start. Staff-assisted services are available for all external customers in order to expedite the processing of your instrument usage request (as an alternative to the slower process of needing to complete facility trainings and orientations).
  • Our team will verify the information and then work with you to schedule training for instruments you request access to.
  • You must complete training for any instruments you request access to.
  • Our team will grant you access to the instruments via the reservation system and to the lab space via our building manager(s).
  • Your continuing usage of our instruments is an implicit acceptance to abide by the general rules we have laid out above.



The instrument reservation system is our primary method for allowing all users to view machine availability and to block off time for their exclusive use. We ask all users to please book their time on .

As instrument usage has grown over the last few years, we have also implemented reservation limits and cool-off times for individual users, in order to assure that the instruments are shared by the community. This said, we understand that some experiments may be more demanding and can grant longer reservations on a case-by-case basis if you write: 



Illumina NextSeq 2000

25 h

Illumina MiSeq

25 h

10x Chromium Ctrler

4 h

Agilent TapeStation

2 h

BioRad CFX384

2 h

When you arrive at the instrument, please complete the paper-based usage logs next to the instrument with information on your experimental run.



Please do not install any programs, apps, or third-party software on the computers without expressed approval by any of the core staff.



All users are responsible for maintaining copies and backups of their data. For Illumina sequencers (MiSeq, NextSeq 550), your data is automatically transferred to your personal BaseSpace cloud account as it is being generated during a sequencing experiment. Please note that no local copy of the data is stored or archived on the sequencer.

All other instruments (BioRad CFX384, TapeStation) generate raw data files that are saved locally on the computer attached to the instrument. As a courtesy, we will retain these data files for up to 12 months after the experiment, but we encourage all users to immediately transfer or back up your data. Needless to say, please do not delete or move any files that do not belong to you!

Because of the risk of viruses and malware, USB connections (flash/thumb drives and portable HDs) are absolutely prohibited.



Our staff will collect usage logs (paper and electronic) and use these to calculate billable amounts for each research group. This will be done the first week of every month for the previous month, and will follow the most up-to-date fees schedule.

For internal users, FAS account transfers will occur within 5d after the statement date (typically in the middle of each month).

If there are any disputes regarding the invoice or billing details, please contact core staff.



We understand that unexpected events or sample processing delays may impact your experimental plans. Especially in the case of our heaviest-used instruments, we also need to balance a desire to provide flexibility against the disruption in somebody else’s studies when they had to plan around your calendar hold. As such, we have instituted the following cancellation policies for our instruments.




Illumina NextSeq 550

24h before reservation

Price of 1 run

Illumina MiSeq

24h before reservation

Price of 1 run

10x Chromium Ctrler

24h before reservation

Price of 1 run

Agilent TapeStation

4h before reservation

Price of 10 samples

BioRad CFX384

4h before reservation

Price of 1 plate

*We are willing to consider forgiving cancellation charges on a case-by-case basis. For such, please contact our core staff with an explanation of your situation, the instrument reservation slot involved, and the circumstances that led to your inability to cancel a reservation ahead of these limits.



When users overbook instruments, they block off time that could have benefited another user. Again, there is a balance between affording someone flexibility in recognition of a complicated or demanding sample preparation workflow, versus disrupting or inconveniencing other users. This is a particular problem for the Illumina sequencers, which are heavily used.

As such, if a user books the Illumina MiSeq or NextSeq 550 for >30h, we will assume that the user has run 2 experiments and bill accordingly.



We remind all users that certain behavior and practices can adversely impact other users’ experience with our core and the instruments, and may also introduce additional inconveniences for our staff. Our staff have agreed on a ‘three-strikes’ policy that will define how we will respond to violators of the basic rules we laid out above.

  • WARNING: We get it, mistakes happen. In this case, we will send an email reminder of the rules and what you agreed to abide by when you decided to use the core facility.
  • FIRST OFFENSE: We will email you to detail what you forgot to do and what we expected. We will also describe what might happen should you fail to correct your behavior (or inaction).
  • SECOND OFFENSE: We will notify both you and your PI of the repeat offense, and remind you of what we will do if you fail to correct your behavior.
  • THIRD OFFENSE: We will block your access to the core facility for two months. This includes revoking your access to the lab space, removing all of your existing future reservations, and also preventing you from reserving all core instruments.

In our experience, users who are discourteous and repeatedly violate rules for one instrument are likely to do the same for our other instruments, so while full facility restrictions seem heavy-handed, we find this to be a reasonable final response.

The exception is if a user is found to have damaged an instrument due to negligent usage or failure to adhere to established operating protocols. In this case, we will escalate immediately to the third strike and suspend your access to the core indefinitely.



A university-wide central shared research facility is one that is available to all faculty members and associated personnel on a first-come, first-served basis. In order to maintain state-of-the-art facilities on campus, it is necessary that all core facility users exhibit good citizenship and take care of our shared resources. Standard operating procedures specific to each core must be followed, including the completion of all required training necessary for use of each machine or technology. Additionally, users should adhere to any further directions given by core technical directors or staff.

Damage to an instrument or instrument malfunction must be reported to core staff immediately. Failure to do so may compound damage and expense. Minor damage may be covered by the core. Instruments require regular service and repair and these costs are built into the normal rates. However, PIs will be responsible for covering significant damage to equipment resulting from user negligence.

In the event of damage to an instrument that clearly resulted from a user’s failure to adhere to established operating protocols then the user’s principal investigator will be expected to pay for repairs not covered by service contracts. Our staff will notify the lab’s PI of the incident and charges.



In order for us to continue to demonstrate our value added to the university community and to justify equipment purchases and upgrades, we really appreciate your acknowledgments of our core facility and staff in your publications and presentations. Listing the equipment used in the Materials & Methods section will also help us further understand how each of the instruments aligns with the scientific output of the university community.

[Technique/Technology] was performed at the Single Cell Immunophenotyping Core of the University of Chicago” and “We are grateful to the University of Chicago’s Single Cell Immunophenotyping Core Facility, especially [Staff Name], for their assistance with [Technique/Technology].” If you are so inclined, we welcome you to send us details of your publications and conference proceedings that were made possible with the core facility!



Institution: The University of Chicago

  • School/Division: Pritzker School of Molecular Engineering
    • Research Center: Chicago Immunoengineering Innovation Center


Lab Location: KCBD 10220E, 900 E 57th St, Chicago, IL 60637

Core Staff: Refer to core facility website for the latest roster.

Emailing the Core:


Mailing List Email: