Picking the fluorochromes that work well together in a multi color experiment is very important. We will help you with this task when discussing your experimental plan, but if you would like to be proactive, here are some links where you can get an idea how the various fluorochromes might work for you.

Keep in mind that the Canto II is equipped with a 488 and 633 nm laser, detection from the blue laser at 780/60, 702/65, 632/45, 585/42, 530/30; detection from the red laser at 780/60, 710/50, and 660/20

Excitation possibilities on the LSR II are: 404, 488, and 633 nm. Basic set up of detectors from the violet laser: 610/15, 525/50, 450/50; from the blue laser: 780/60, 710/50, 688/15, 610/20, 575/26, 530/30; from the red laser: 780/60, 730/45, 660/20. Do not reorganize filters without consulting Core Facility personnel.

To view individual fluorescence spectra of various fluorochromes look at the following Invitrogen link. An alternative to the above link can be found on the BD website.

To see how the individual dyes work together and with our machines follow this Invitrogen link (you will need Java for this).

The fluorochromes one can use in an experiment are limited by the availability of reagents as well as the instrumentation. The following chart is designed to give you an idea about commonly used reagents in 6, 8 and 10 color experiments.

Quantum dots (Qdots) might be the future of fluorescence based detections. Qdots are excited over wide range, have a narrow and bright emission spectrum with minimal photo-bleaching. To learn more about Qdots click here.

6-Color	8-Color	10-Color
FITC or Alexa 488	FITC or Alexa 488	FITC or Alexa 488
PE	PE	PE
-	-	PE-Texas Red or PE-Alexa 610
PerCP-Cy5.5	PerCP-Cy5.5	PerCP-Cy5.5
PE-Cy7	PE-Cy7	PE-Cy7
APC or Alexa 647	APC or Alexa 647	APC or Alexa 647
-	-	Alexa 680 or 700
APC-Cy7	APC-Cy7	APC-Cy7
-	AmCyan	AmCyan
-	Pacific Blue	Pacific Blue