Flow Cytometry Users Guide


A complete ‘ish’ guide to Flow cytometry or FACS for cell cycle work.

Covers all aspects from tissue culture, through to running and analyzing your samples on a FACScan or FACS Calibur.

It was written by me a few years ago and so is a bit out of date.  For example there is a new “prettier” version of CellQuest (Pro) now in use, but essentially it is still the same.

Download basic templates and Settings for 1D and 2D FACS using Cell Quest Pro
Please note that you will need to rename the extensions from .doc to .zip then extract the files as normal:      

Templates              Settings

16 responses to “Flow Cytometry Users Guide”

  1. Christina says :

    Gee whiz, and I tohuhgt this would be hard to find out.

  2. Martin Fitzpatrick says :

    Hi Andrew. I’m putting together a site of ‘smart’ lab protocols to allow better time management in the lab – and provide visual tips/etc. while working; as well as access via mobile app with calculation help etc.

    I would like to use your guide to build a set of flow cytometry protocols for this purpose – credited and linked back here of course. Would that be ok?

    If it’s not clear what I’m talking about I can do a quick demo for you.

    Thanks for this great resource

  3. ScienceTechBlog says :

    Sure no problem. I wrote the guide to help people out and the more that see it and get help from it the better. Its great to get credit for it, but that was not my goal for writing it.
    Good luck and happy FACSing.

  4. Tony says :

    It takes real skill to work humor into a FACS protocol.

    Well done Sir. Well done.

  5. tralala says :

    i can not open the files in windows 7, can you please upload them in doc format as well, will appreciate too much 🙂 (i first converted to zip then extracted files but the files are not doc. )
    thnaks in advance

  6. tralala says :

    aha sorry i didnt see the pdf:)

    guys for who makes same stupid mistake as me, just click on preview of the file you ll get the pdf

    thank you so much:)

  7. M says :

    Hi Andrew,
    Been reading through your (very useful) guide and have a question – on P9 point 4) you say that a change in the number of cells will shift the profile left or right. Is this from personal experience or do you know of a reference for this? I am experiencing this and would like to know more, but can’t find any details anywhere.
    Many thanks,

    • ScienceTechBlog says :

      Hi its a simple dilution problem. That is the more cells you have the less amount of PI per cell which will reduce the intensity of the staining thus shifting the cells to the left. The opposite occurs if you have far less cells. I don’t know of any references for this effect, its purely from personal experiance.

  8. M says :

    Thanks Andrew, this has been bugging me for a while!

  9. Zhila says :

    I work on ploidy level of Vitis vinifera by flowcytometry and I need a perfect completely protocol for this. Please send me. Thanks.

  10. Zhila says :

    I need a method for determination of ploidy level in plants by flowcytometry with its details.thanks

  11. Purushotham Reddy says :

    Thank you for your time and help by putting up this protocol together!

  12. Delia says :

    I’ve been trying to put together a DNA cycle experiment using FACScan for a few months now and your tutorial has helped a lot!!
    I downloaded the settings you provide for DNA and the file is empty. Since I could see the settings for GFP-PI I think there is some sort of problem with the file. My other question is do you think I could use these settings in FACScan? The GFP-PI settings file specified that is for FACS Calibur.

    Thanks for all the information you put together here it has been super helpful!

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  1. Flow Cytometry User Guide « ScienceTechBlog - July 18, 2011

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