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Flow Cytometry Shared Resource Center at Johns Hopkins Medicine

Johns Hopkins Medicine Campus

We are located on the 10th floor of the Richard Starr Ross Research Building (Room S1071A). The Core is managed by Division of Hematology, Department of Medicine. The Core offers state-of-the-art flow cytometry cell analysis and high-speed sorting to the research community at Hopkins.

We are currently equipped with BD FACSAria IIu Cell Sorter with three lasers (405-, 488-, and 633 nm) (9 Colors) capable of 4 way sorting. The Core is also equipped with analyzers: Cytek Aurora with four lasers (405-, 488-, 561-, and 640-nm) (48 fluorescence channels and three scatters); BD LSR II with four lasers (355-, 405-, 488-,and 633-nm) (13 colors) and BD FACSCalibur with two lasers (488 nm and 633 nm) (4 colors).



All analyzers are accessible for unassisted use 24 hours a day, 7 days a week.

Please acknowledge the use of the JHU Ross Flow Cytometry Core in your publications. If you used Aurora, please cite “Aurora is funded by a NIH Grant (S10OD026859).”

  • The FACS Aria sorter equipped with three lasers (405-, 488-, and 633-nm), which allows up to 9 fluorescent parameters (Configuration). FACS Diva software (v6) is used for cell collection and analysis. It was upgraded to the level of II in July 2012. The sorter is operated by a designated operator, and able to sort 4 different cell populations simultaneously. It is operated under the BSL2, and applicable to sorting both human and rodent cells (see Biosafety Policies).

  • Aurora is a spectral flow cytometer. It is a four laser-system (405-, 488-, 561-, and 640-nm), and is equipped with an integrated high throughput sampler (HTS) for 96-well plate (U, V, and flat bottom). This cytometer has three scatters (488-nm FSC and SSC, and 405-nm SSC), and 48-fluorescence channels (4-laser Fluorochrome Guideline).  In addition, Aurora has the capability to analyze small particles (virus, mitochondria, exosomes, and extracellular vesicles, etc.). SpectrotFlo software is used for data acquisition and analysis.

    Aurora can give superb resolution of dim and rare populations, minimal fluorochrome overspill, excellent auto-fluorescence subtraction, and control library. You can use any fluorochrome (emission wavelength between 365 to 829-nm) excited by the onboard lasers with one configuration for all assays, no need to change optical filters for any fluorochrome.

    Citation Policy: This is a NIH SIG S10 granted (2019) instrument. All users who used this instrument must have acknowledgments of the S10 grant in your scientific publications.

  • The LSR II is equipped with four lasers(UV 355-, 405-, 488-, and 633-nm),  (Configuration and Fluorochrome Chart). FACS Diva software (v8) is used for data acquisition and analysis.

  • The FACSCalibur is equipped with two lasers (488- and 633-nm). Four channels can be set for fluorescent parameters (Configuration). CellQuest software is used for sample acquisition and data analysis.


Billing Policies and Fees

  • User will be billed the maximum of either time reserved or actually used on the instrument, rounded up to the nearest 30 minutes for Calibur or nearest 15 minutes for Aurora and LSRII. The minimal usage per session is 30 minutes on all analyzers, and 60 minutes on sorter

    • Calibur: $60/hr.
    • Aurora or LSR II: $100/hr.
    • Aria II Sorter:
      • $80 setup fee$120/hr. (11AM-5PM)
      • $180/hr. (5PM-7PM)
      • $300/hr. (7PM-9PM)
    • Analyzer Training: $200 (Aurora) + Instrument Usage
    • FlowJo: Free (Ross Flow Core Users)
    • Policy Orientation Only: $60


    Analyzers are self-analysis instruments. Staff assistance for Aurora and LSR II can be requested by appointment with additional fee.

    Training for Analyzers

    Policy orientation is a mandatory requirement to every user. Technical training is optional if you are able to work independently on the analyzers. Technical training session includes instruction on the operation of the instrument and the use of the software


    Consultation for multi-color panel design and other flow cytometry questions are limited to our core users only.

  • Cancellation and Modification

    Reservations for analyzers must be canceled or modified at least 24 hours before the scheduled time. Reservations for Aria sorter must be canceled or modified at least 48 hours (2 business days) before the scheduled time. Failure to cancel will result in charges for the full time reserved. For cancellations time without filling by other use, the user will still be billed. There is a cancelation fee for first schedule on Aria sorter

    Late Arrivals

    Late arrivals interfere with subsequently scheduled activity; the user will be billed from the start of the time reserved to the actual finish time. The next user scheduled after a late arrival user has the right to start at their scheduled start time. The late arrival user should make provisions to rebook an open time slot.

    Data Storage

    It is the user’s responsibility to copy, transfer, and store data at your own storage immediately after done. Core will delete data periodically from software and from the computer without notice, and is not responsible for any data loss, including computer crash.


Biosafety Policies

The Flow Cytometry Core is a BSL-2 Facility to handle human cells, and subject to the rules, regulations, guidelines that apply to the use of biohazardous materials in all research laboratories. As a multi-use facility, anyone using the facility must have their proposal approved separately by the IRB (human), Animal Review Committee, and Biohazards Review Committee. The RFCC Director, Manager and staff members undergo training sponsored by the Dean’s Office in use of human subject materials, animals and biohazards. Our Core asks all investigators to review and comply with the Biosafety requirements of Johns Hopkins University, and checks that their approvals are current, but is not involved with the applications for the individual users.

The current setup for the core prevents us from running samples that contain radioactivity or potentially infectious agents to humans.



  • All users must register for an account on iLab:

    1. Navigate to the core page:
    2. In the upper-right-hand corner of the screen select ‘Register using JHU Credentials’.
    3. You will be directed to an authentication page to enter your JHED ID.
    4. Once you have entered your credentials, click the ‘Login’ button.
    5. You will be directed to an iLab Registration page to select your PI/Lab, and verify your contact information.
    6. Once your registration has been submitted, your PI will receive a notification that you have requested membership to their lab in iLab.  PI will need to approve membership and assign any Cost Objects for use

    Once you have been accepted into your PI’s lab and assigned Cost Object, please use your JHU E-mail to contact Xiaoling Zhang ( for Sorting or Dixie Hoyle ( for Analyzer Policy Orientation and/or Technical Training.  After you have iLab account, cost object, and completed policy orientation and/or technical training, you will be an authorized user.

  • For authorized analyzer users to schedule time on instruments on iLab:

    1. Navigate to the core page:
    2. At the upper right hand of the page select sign in, enter your JHED ID and password.
    3. Select the Schedule Equipment tab and click on the ‘View Schedule’ button next to the instrument of interest.
    4. To request a reservation, click and drag to select the time frame from the available schedule.
    5. A window will pop up that will allow you to verify your reservation details and provide Cost Object before saving the reservation

Contact Information

Please do not hesitate to contact us if you have any questions about potential uses of flow cytometry for your research projects, how to appropriately design panels for flow cytometry, how to analyze flow data, and prepare for sorting.  We also provide data acquisition and analysis completed by Core staff if you have little flow background and short projects.

  • Ross Building, Room S1071
    720 Rutland Ave
    Baltimore, MD 21205

    Zack Wang, PhD, Director
    Office: Ross 1029

    Xiaoling Zhang, MD, MS, Manager

  • Robert Brodsky, MD
    Director, Division of Hematology
    Professor of Medicine and Oncology

    Linzhao Cheng, PhD
    Professor of Medicine

    Jeffrey Smith, M.A.
    Sr. Administrative Mgr., SKCCC Research Services & Shared Resources
    Asst. Director, SOM Office for Faculty Research Resources

    Mark Soloski, PhD
    Bayview Flow Core Director
    Professor of Medicine



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