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UAB Institutional Research Core Program Office of Research

UAB Institutional Research Core Program

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    Flow Cytometry and Single Cell Core Facility
  • Flow Cytometry and Single Cell Core Facility
  • Flow Cytometry and Single Cell Core Facility
  • Flow Cytometry and Single Cell Core Facility
  • Flow Cytometry and Single Cell Core Facility
  • Flow Cytometry and Single Cell Core Facility
  • Flow Cytometry and Single Cell Core Facility

Policies

  • Flow Cytometry Services

    Flow Cytometry Services

    1. New users:
      1. New users will request access to the scheduler (FBS system) by emailing This email address is being protected from spambots. You need JavaScript enabled to view it.. Please provide the following details in the email.
        1. Your full name
        2. PI Name
        3. PI Department/Division
        1. Analyzers: All the analyzers are self-operated. New users interested in utilizing the technology must coordinate training with FCSC staff. Availability for training sessions should be discussed directly with staff. Typically, the initial training session lasts for approximately 2 hours. Additional training sessions will be scheduled based on the user's prior experience with flow cytometry, as determined by FCSC staff. Following completion of training, users must undergo a practical test to demonstrate proficiency in operating the instrument independently. Access to the instrument will be granted upon successful completion of the test. New users must reserve instruments during regular work hours (9 AM to 5 PM, Monday to Friday) for at least five appointments before requesting after-hour access (before 9 AM and after 5 PM, and on weekends).
        2. Sorters: Sorting is offered as an assisted and self-run service. Assisted sorting appointments will be made on the FBS scheduler at least 24 hours before the planned sorting experiment. To ensure availability, assisted sort requests on short notice must be discussed with the staff. Investigators requesting self-run access to the sorters will complete the training. After completing the training, the investigators must self-sort at least 20 hours during business hours to be granted after-hour access.
      3. Please provide the following information to request after-hour access.
        1. Your full name:
        2. PI name:
        3. PI Department/ Division:
        4. Blazer ID:

    2. Cancellation policy:
      1. Analyzers and sorters: Investigators are allowed to cancel an appointment for analyzers before 12 hours and for sorters before 48 hours of the scheduled appointment without any charge. Cancellation within 12 hours prior to the appointment for analyzers and 48 hours for sorters will be charged in full. Under exceptional circumstances, the cancellation fee may be waived at the discretion of the FCSC staff.
      2. Missed appointments will be fully charged.

    3. Biosafety:
      1. Both facilities at Shelby and Bevill are designated BSL2 facilities. Investigators accessing the facilities will follow the UAB-approved protocols for biosafety.
      2. Personal protective equipment will always be worn while using the facility.
      3. Users are responsible for providing FCSC staff with information about the infectious nature of samples.
      4. The UAB Environmental and Occupational Safety should approve sorting protocols for infectious samples before scheduling the appointment.
      5. Investigators working with bacteria and yeast requiring sorting services should discuss with the FCSC staff before scheduling appointments.
      6. Sorting bacteria/yeast may require additional cleaning and culture steps, which will be performed by the FCSC staff and may take up to 1 to 4 hours. These charges will be billed to the investigators requesting the services.
      7. Investigators using the facility will maintain the cleanliness of the shared resource. All the samples will be properly disposed of in the designated biohazard labeled bins by the investigators using the facility.
      8. UAB public health protocols will be implemented at the facility.

    4. Software:
      UAB has a site license for the FlowJo™ analysis software. Investigators will be billed annually to access the software. The software price may vary yearly depending on the number of licenses on the campus. Please contact This email address is being protected from spambots. You need JavaScript enabled to view it. to gain access to the software or if you have other inquiries. Investigators may access ModFit LT and Ideas software at the dedicated workstation at the FCSC.

    5. Data storage policy:
      The FCSC is not responsible for the storage of the data. Investigators should retrieve the raw data and the experiment templates immediately after the experiment's conclusion. The data from the computers will be deleted periodically without notice.

    6. Billing:
      1. The time billed for an appointment will be the total time used (rounded to the closest 15-minute increment) or the time reserved, whichever is longer.
      2. Investigators using the instrument without reservation on the FBS calendar will be charged an additional 15 minutes on each such usage.
      3. The billing for the previous month will be concluded within the first three weeks of the current month. For example, the invoices received by the investigators during February will be for usage in January.
      4. Investigators will have five working days to request any changes in the invoice, such as changing the account number to be billed.
      5. If the investigator would like to challenge the incurred charges, they may do so within five working days of the invoice date. After that, the charges are finalized and will not be revisited.
      6. External (non-UAB) investigators using the FCSC facility services will be subject to an additional 48.5% indirect costs (IDC).
      7. Investigators must try to resolve any defaults to avoid service disruption. All outstanding issues must be addressed promptly to maintain the integrity and continuity of service.

    7. Questions and concerns:
      1. Sorting: It is recommended that a post-sort purity test be performed after each sort. Investigators must work with the FCSC core staff to troubleshoot any low-purity sorts.
      2. Investigators having questions regarding the usage of the facility should email This email address is being protected from spambots. You need JavaScript enabled to view it..
      3. Investigators concerned about proceedings at the core should contact the facility manager.

    8. User compliance:
      The FCSC has the right to refuse services for investigators who show noncompliance with the policies.

    9. University holidays and bad weather closings:
      1. The FCSC will be closed on the University designated holidays.
      2. The FCSC will be closed if the University closes due to inclement weather conditions. All the assisted appointments will be canceled.

    10. Audio-Visual Recording Policy:
      Due to data security and personal privacy concerns, the FCSC strictly prohibits using audio-visual recording devices within the premises without prior written approval from the Facility Manager.

    11. Acknowledgments:
      Investigators using the facility should acknowledge FCSC and the support of the Center for AIDS Research grant AI027767 and The O'Neal Comprehensive Cancer Center grant CA013148.
  • Single Cell Services

    Single Cell Services

    1. New users:
      Investigators who are new to utilizing single-cell services at the Flow Cytometry and Single Cell Core (FCSC) facility are advised to contact the single-cell core staff to arrange a required briefing session. New users will request access to the scheduler (FBS system) by emailing This email address is being protected from spambots. You need JavaScript enabled to view it.. Please note the following details in the email. i. Your full name ii. PI Name iii. PI Department/Division

    2. Single Cell Services instrument usage policy:
      The Single Cell Services of the FCSC offer various technologies to the investigators. The usage policies for single-cell instruments at FCSC are as follows:
      1. Assisted services: Assisted Services refer to a comprehensive support model provided by the FCSC facility, where the core staff takes responsibility for conducting single-cell experiments from the moment the investigators submit samples. This full-service approach is designed to ensure that all aspects of the experiment, from setup to library preparation, are expertly managed by the facility's personnel.
        A more collaborative approach may be necessary in certain complex single-cell experiments, such as CITEseq. These instances require the active involvement of the investigator alongside the core staff to address the specific needs and intricacies of the experiment effectively. Investigators are encouraged to consult with core staff to understand the extent of engagement needed, as the level of complexity and the requisite effort from the investigators can vary significantly depending on the nature of each experiment.
      2. Unassisted services: Unassisted services pertain to the use of certain core facility’s single-cell analysis equipment that investigators can operate independently. The core facilitates this self-service model, allowing researchers direct access to specific instruments listed in the table (Table .1.).
        To qualify for unassisted use of the equipment, investigators may be required to undergo training sessions. The aim of these sessions is to ensure users achieve a threshold competency level necessary for the safe and effective operation of the instruments. The exact number of training sessions and the specific competencies required can vary based on the equipment and the complexity of its operation. Investigators interested in utilizing unassisted services are advised to consult with core staff to ascertain the training requirements and to ensure they meet the necessary criteria for independent access to the equipment.

      Table.1.
      Instrument Assisted Services Unassisted Services
      10x Chromium Offered Offered
      10x Visium Offered Not-offered
      10x Xenium Offered Not-offered
      BD Rhapsody Offered Offered
      Fluidigm C1 Offered Offered
      Biomark HD Offered Offered


    3. Appointments:
      Investigators seeking to conduct experiments with FCSC single-cell services must arrange their appointments directly with the facility's staff. Regular appointment scheduling is available from Monday to Friday, between 9 AM and 5 PM. In exceptional circumstances, assisted analyses may be conducted after hours (after 5 PM or before 9 AM and on weekends). Still, such arrangements need to be discussed and confirmed with the core staff well in advance. For experiments requiring cell sorting, it is essential that investigators book the necessary sorter time through the facility's scheduling system.

    4. Cancellation policy:
      Investigators may cancel single-cell appointments up to four hours before the scheduled time without incurring charges. Cancellations made within the 4-hour window prior to the appointment will incur a waiting fee ($75 per hour) for up to a maximum of 4 hours. In the case of no-show appointments, a charge equivalent to 4 hours of waiting time will be applied at a rate of $75 per hour. Canceled single-cell experiments will still incur the charges for sorting appointments. Please refer to the flow cytometry services cancellation policies for further details.

    5. Library storage policy:
      1. Duration of Storage: The FCSC facility will store completed single-cell libraries in the core freezer for a period of up to 6 months.
      2. User Responsibility: Users are encouraged to coordinate with the FCSC single cell services staff to collect their libraries post-completion for storage in their respective lab freezers.
      3. Maintenance and Disposal: The FCSC facility will conduct regular cleanings of the refrigerator. Any libraries that remain unclaimed past the 6-month storage period may be discarded during these maintenance sessions.
        Users are advised to adhere to this policy to ensure the safekeeping and integrity of their single-cell libraries.

    6. Policy on experiment failure and cost recovery:
      The FCSC facility staff is dedicated to ensuring the success of all single-cell experiments conducted within our premises. However, we recognize that not all experiments may achieve the intended results, potentially due to various unforeseen issues such as microfluidics chip failures or instrument malfunctions.
      1. Consumable Reimbursement:
        Should an experiment's failure be attributed to compromised consumables, our team will make efforts to recuperate these costs from the respective vendors. It is important to note that the FCSC cannot assure full reimbursement of consumable expenses from vendors in every instance.
      2. Investigator Discretion:
        Investigators retain the discretion to proceed with experiments, even when FCSC staff advise otherwise based on preliminary assessments. It is understood that any costs arising from potential experiment failures under such circumstances will not be the responsibility of the FCSC.
      3. Liability for Failed Experiments:
        The FCSC will not bear responsibility for any financial losses incurred by investigators due to experiment failures.
        This policy aims to clarify the roles and responsibilities of both FCSC staff and investigators in the conduct of single-cell experiments, ensuring a transparent and collaborative research environment.

    7. Data storage policy:
      The FCSC is not responsible for the storage of the data. Investigators should retrieve the raw data and the experiment templates immediately after the experiment's conclusion. The data from the computers will be deleted periodically without notice.

    8. Billing:
      1. The billing for the previous month will be concluded within the first three weeks of the current month. For example, the invoices received by the investigators during February will be for usage in January.
      2. Investigators will be provided five working days to request any changes in the invoice, for example, changing the account number to be billed.
      3. If the investigator would like to challenge the incurred charges, they may do so within five working days of the invoice date, after which the charges are finalized and will not be revisited.
      4. External (non-UAB) investigators using the FCSC facility services will be subject to an additional 48.5% indirect costs (IDC).
      5. Investigators are required to make every effort to resolve any defaults to avoid disruption of service. It is imperative that all outstanding issues are addressed in a timely manner to maintain the integrity and continuity of service.

    9. Biosafety:
      1. Both facilities at Shelby and Bevill are designated BSL2 facilities. Investigators accessing the facilities will follow the UAB-approved protocols for biosafety.
      2. Personal protective equipment will always be worn while using the facility.
      3. Users are responsible for providing FCSC staff with information about the infectious nature of samples.
      4. The UAB Environmental and Occupational Safety should approve protocols for infectious samples before scheduling the appointment.
      5. Investigators using the facility will maintain the cleanliness of the shared resource. All the samples will be properly disposed of in the designated biohazard labeled bins by the investigators using the facility.
      6. UAB public health protocols will be implemented at the facility.

    10. User compliance:
      The FCSC has the right to refuse services for investigators who show noncompliance with the policies.

    11. University holidays and bad weather closings:
      1. The FCSC will be closed on the University designated holidays.
      2. The FCSC will be closed if the University closes due to inclement weather conditions. All the assisted appointments will be canceled.

    12. Audio-Visual Recording Policy:
      Due to data security and personal privacy concerns, the FCSC strictly prohibits audio-visual recording within the premises without prior written approval from the Facility Manager.

    13. Questions and concerns:
      The investigators, with any questions or concerns regarding single-cell services, should contact the Associate Director of the single-cell services.

    14. Contacts for single-cell services:
      Investigators utilizing the single-cell services should contact Dr. Shanrun Liu (This email address is being protected from spambots. You need JavaScript enabled to view it.), Dr. Joe Sun (This email address is being protected from spambots. You need JavaScript enabled to view it.), or Dr. Madhubanti Basu (This email address is being protected from spambots. You need JavaScript enabled to view it.) for consultation.

    15. Acknowledgments:
      Investigators using the facility should acknowledge FCSC and the support of the Center for AIDS Research grant AI027767 and The O'Neal Comprehensive Cancer Center grant CA013148.
  • COMET Services

    COMET Services

    1. Assistance and Contact:
      1. All COMET runs are considered assisted services.
      2. Users must contact the Flow Cytometry and Single Cell Core Facility (FCSC) at This email address is being protected from spambots. You need JavaScript enabled to view it. to develop the COMET Usage Plan.

    2. COMET Usage Plan:
      1. Goal: to outline the optimal utilization of COMET staining platform and downstream analysis.
      2. Usage Plans will outline:
        1. Samples
          • Submission form
          • Sample preparation
          • Quality Check
        2. Antibody Panels
          • Addition of new antibodies
          • Pricing
        3. Data handling
        4. Analysis plan

    3. Samples:
      1. Submission:
        1. All users must complete the sample submission form, providing comprehensive details about their samples (request form at This email address is being protected from spambots. You need JavaScript enabled to view it.).
        2. The form should include relevant information to facilitate the staining process effectively.
      2. Preparation:
        1. Investigators are responsible for preparing and positioning samples as per the guidelines provided by the facility.
        2. Proper preparation is crucial for optimal staining results.
      3. Quality Check:
        1. It is the responsibility of the users to verify the quality and positioning of their samples before processing.
        2. A preliminary analysis of H&E staining on serial sections is recommended.
        3. The area of interest should be within the imaging window on the COMET.
        4. Users will be charged for slides if the staining protocol fails due to poor quality of tissue section or improper positioning.

    4. Antibodies and Panels:
      1. The antibody bank lists various antibodies and panels that have been tested and optimized on mouse or human tissues. Requested antibodies/panels will be tested and optimized on investigators' samples before processing the full cohort for staining.
      2. Addition of New Antibodies
        1. The addition of investigator’s choice of a new antibody to existing panels requires optimization for staining conditions.
      3. Staining Assessment and Optimization:
        1. Upon completion of staining on the investigator's optimization slide, data will be transferred to the virtual computer drive.
        2. Investigators are required to assess staining specificity and patterns promptly.
        3. Recommendations for changes in the staining protocol should be communicated as soon as possible for further optimization or running on the rest of the slides.
        4. Once the staining protocol is finalized and applied to all requested slides, data will be transferred to the virtual computer drive for user access.

    5. Data Handling:
      1. User Responsibility for Data Management:
        1. UAB-FCSC is not responsible for the storage or management of user data for an extended period.
        2. Users must adhere to NIH data management guidelines.
        3. It is the user's responsibility to back up and store data appropriately.
      2. Data Size and Periodic Removal:
        1. Multiplexed staining of a single slide generates big data file (approx. 100 GB of data/slide) depending on the staining protocol.
        2. Once confirmed by the user for full accessibility, data will be periodically removed from the COMET computer to free up space for further use.

    6. Analysis:
      1. Image Analysis resources are provided including:
        1. Computing Hardware through Virtual Access on Azure Computers
        2. Horizon Viewer
        3. Visiopharm Analysis Software
        4. Software Training
        5. Support for analytical design and execution

      2. Azure Core Computing Systems
        1. The Azure computers (2) are highly equipped data analysis computers with substantial CPU and GPU hardware, 30TB of shared storage and pre-installed analysis software.
        2. Limited Computer Storage:
          • Users share limited computer storage space.
          • Data can only reside on the virtual computer drive during analysis and must be removed upon project completion.
          • Extended storage on the virtual computer drive will result in additional charges determined by the FCSC.
        3. Computing Time Reservation:
          • Users are required to reserve computing time on the Facility Booking System (FBS) to access the UAB Azure Image Analysis Computer – The virtual computer.
        4. Logout Procedure:
          • Users should be aware that closing the Citrix server alone or allowing it to time out does not constitute a proper logout.
          • Users are responsible for ensuring all analyses and software are closed before logging out to free up resources for others.
          • Users who do not adhere to the logout procedures will be charged accordingly.

      3. Visiopharm Analysis Software
        1. Is a high end image analysis software specialized for histopathological image analysis including COMET mIF images.
        2. Interface Usage:
          • Upon completion of the reservation time, users must actively close the Visiopharm user interface.
          • Failure to close Visiopharm blocks the seat for other users and may result in charges
          • Failure to logout effectively blocks the seat for other users and may result in charges.

      4. Access Request and Training:
        1. Users must request access to the necessary image analysis software.
        2. It is the user's responsibility to ensure they have access to the required software and undergo necessary training for staining assessment and analysis.

      5. Training Resources:
        1. Image analysis training resources, including videos, are provided by Visiopharm on the Customer Portal.
        2. Recordings of training sessions are also available on the official website for reference.
        3. Two one-hour bi-weekly shared Visiopharm office hours are provided. Recordings are made available.