Flow Cytometry

@ The Scripps Research Institute

Spectral Cytometry

The Aurora is the Flow Cytometry Core Facility's newest flow cytometer. This analyzer detects the entire spectral fingerprint of each fluorophore, allowing for more flexibility, sensitivity, and accessibility in panel design.
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Analyzer Calendar

Use the calendar to reserve analytical cytometers for your data acquisition. Each lab has a single login for their lab members to use.
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Learn about flow cytometry and find tools that may be useful to your experiments.
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Policies & Guidelines

⚠ Lab Safety

All flow core equipment resides in laboratory space. Therefore, all laboratory rules as mandated Environmental Health & Safety apply. Failure to adhere to these rules at all times will result in suspension of access to all flow ctyometry core facility equipment.

All users must be up to date with lab safety training. Use of unfixed human samples (or other BSL-2 level material) in the flow core require approval. BSL-3 and radioactive samples are not allowed in our facility under any circumstances.

Correct PPE must be worn and proper containment procedures must be practiced at all times in this location. Specifically:

  • All BSL-2 samples must be transported to this location in a secondary, waterproof container with a secure lid (such as a tupperware, styroform is not acceptable).
  • Closed toe shoes are required in this location at all times.
  • The cytometer workstations are considered lab space, including the computers used to collect data. Therefore, gloves should be used when operating the keyboard and mouse.
  • Absolutely no laboratory materials (samples, gloves, labcoats, etc) are allowed in the staff office, as it is a "clean area". Please avoid touching door handles, light switches, elevator buttons, etc. with gloves on.


General Rules

Proper usage and routine cleaning of the equipment are critical for optimal data collection. This equipment is shared between many users, so it is imperative to treat it as if it were your own. Although calibrations and other maintenance procedures are the responsibility of the flow core staff, it is important that users properly perform the startup, shutdown, and cleaning procedures as described in the training sessions. For more information on user responsibilities, please click here.

Failure to comply with all usage procedures as laid out in the equipment tutorials, manuals, and training sessions can result in restricted or suspended access to all flow core equipment.

Users are responsible for bringing their own supplies. A couple of FACS tubes may be available for cleaning the instrument, but tubes and pipets are not supplied for transferring samples.

The workspace must be cleaned up after each use. Tubes, tips, wipes, and gloves must all be thrown away in biohazard containers and not left at the desk. Spills must be cleaned up or reported.


Data Management

It is the responsibility of all users to copy their data to a secondary, non flow core, medium at the time of collection and/or analysis. Hard drives have crashed, and data has been lost.

We recommend that you bring a USB flash drive every time you use the flow core, whether for sorting, acquisition, or analysis. Even if you forget a flash drive, it is still best to export your data. It will allow you to retrieve it, even if the cytometer is in use. Data may only be exorted

Analyzer data will be purged as needed, starting with the older data, typically data older than one month.

Data generated during sorting will be made available to the user at the time of collection or within 24 hours after collection. Sorter data will typically be housed for a minimum of one month.




Sorts cancelled less than 48 hours in advance will be charged 25% of the time reserved. Less than 24 hours will be charged 50%. To cancel a sort, please email flowstaff@scripps.edu. Billing for sorts begin at the time reserved if the instrument and technician are waiting for your arrival unless a phonecall or email are received before the start of the appointment.


Please update any changes to your analyzer appointments as soon as possible. If you need to cancel, please delete your appointment to free up the instrument for other users. If you do not show up to your appointment, you will be charged for 1 hour.