Fluorophore selection guide for flow cytometry
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- Muriel McCarthy
- 7 years ago
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1 Flow Cytometry Fluorophore selection guide for flow cytometry Dye choices for your instrument made easy
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3 Fluorophore selection guide for flow cytometry Dyes for the 405 nm and 407 nm s Dyes for the 488 nm Dyes for the 635 nm Accuri C6 Flow Cytometer System BD FACSCalibur System BD FACScan Flow Cytometer BD FACSCanto System BD FACSCanto II System, 2- option BD FACSCanto II System, 3- option BD LSR Flow Cytometer BD LSR II Flow Cytometer BD FACSAria Cell Sorter BD FACSArray Bioanalyzer System BD FACSVantage SE Cell Sorter Beckman Coulter Cytomics FC 500 Flow Cytometer Beckman Coulter EPICS XL Flow Cytometer Beckman Coulter Cell Lab Quanta SC Beckman Coulter EPICS ALTRA Cell Sorter Beckman Coulter CyAn ADP Analyzer Beckman Coulter MoFlo XDP Cell Sorter Guava Personal Cell Analysis (PCA) System Guava EasyCyte Mini System Guava EasyCyte Plus System Index
4 Flow Cytometry Fluorophore selection guide Dyes for the 405 nm and 407 nm s Pacific Blue The dye of choice for the first violet channel Excited optimally at ~410 nm with emission maximum at ~455 nm No UV excitation Minimal spectral overlap with green fluorophores Alexa Fluor 405 Excited optimally at ~402 nm with emission maximum at ~421 nm Minimal spectral overlap with green fluorophores Lower in fluorescence than Pacific Blue dye, higher background in some intracellular applications May withstand fixation better than Pacific Blue dye under some circumstances Some UV excitation Pacific Orange Compatible with Pacific Blue dye for multicolor applications of the violet Excited optimally at ~405 nm with emission maximum at ~551 nm Best signal obtained with an RPE emission filter (i.e., 548/42 or 575/26) Qdot 525 nanocrystal Qdot 565 nanocrystal Qdot 605 nanocrystal Allows high level multiplexing with a single excitation source Ultimate in photostability Excited optimally with UV or violet Also excited by every below the emission wavelength Emission centered on the wavelength in nanocrystal name May require cross- compensation depending on fluorophores used Can replace selected energy transfer (tandem) conjugates Qdot 655 nanocrystal Qdot 705 nanocrystal Qdot 800 nanocrystal 2
5 Fluorophore selection guide Dyes for the 488 nm Alexa Fluor 488 Brighter and more photostable than FITC Interchangeable with FITC with only minor changes in compensation Excited at 488 nm with emission maximum at ~519 nm ph insensitive Ideal primary color for flow cytometry RPE (R-Phycoerythrin) Excited at 488 nm or 532 nm with emission maximum at ~575 nm Very bright fluorescence Shows some excitation with 405 nm Highly susceptible to photobleaching RPE-Texas Red Energy transfer dye excited at ~488 nm with emission maximum at ~615 nm Can be measured in FL3 channel on BD and Beckman Coulter instruments RPE-Alexa Fluor 610 Energy transfer dye excited at ~488 nm with emission maximum at ~628 nm Alternative to RPE-Texas Red dye Higher quantum yield than RPE-Texas Red dye with lower compensation against RPE Ideal for use with RPE-Alexa Fluor 700 or dyes in multicolor panels Can be measured in FL3 channel on BD and Beckman Coulter instruments Requires filter modification for optimal use on Beckman Coulter EPICS XL instrument TRI-COLOR Energy transfer dye excited at ~488 nm with emission maximum at ~670 nm Also known as PE-Cy 5 Bright fluorescence Low compensation against RPE Significant emission in APC channel with 633 nm excitation Measured in FL3 channel on BD FACScan and BD FACSCalibur instruments Measured in FL4 channel on Beckman Coulter EPICS XL instrument Can demonstrate monocyte binding in some circumstances continued 3
6 Flow Cytometry Fluorophore selection guide Dyes for the 488 nm, continued RPE-Alexa Fluor 700 Fluorochrome of choice for BD FACSCalibur instrument Energy transfer dye excited at ~488 nm with emission maximum at ~723 nm Very low compensation against FL2 and FL4 when detected in FL3 on BD FACSCalibur or BD FACScan instrument Bright alternative to RPE-Cy 5 (TRI-COLOR, CyChrome, PC5), PerCP, and Together with RPE-Alexa Fluor 610 dye, constitutes the optimal four-color combination using the 488 nm line Energy transfer dye excited at ~488 nm with emission maximum at ~694 nm Lower photostability than RPE-Alexa Fluor 700 Requires more compensation against APC channel than RPE-Alexa Fluor 700 Measured in FL3 channel on BD FACScan and BD FACSCalibur instruments Measured in FL4 on Beckman Coulter EPICS XL instrument RPE-Cy 7 Provides long-wavelength emission off the 488 nm Energy transfer dye excited at ~488 nm with emission maximum at ~775 nm Requires varying degrees of compensation out of RPE channel 4
7 Fluorophore selection guide Dyes for the 635 nm Alexa Fluor 647 Energy transfer dye excited at 633/635 nm with emission maximum at 668 nm An excellent alternative to APC and Cy 5; potentially less background with intracellular staining Brightness comparable to APC in flow cytometry Significantly more photostable than APC and Cy 5 Alexa Fluor 700 Energy transfer dye excited at 633/635 nm with emission maximum at 723 nm Allows three-color analysis using a red when combined with APC and APC-Alexa Fluor 750 Extremely bright and photostable A single, small-molecule direct conjugate alternative to the tandem APC-Cy 5.5 Minimal compensation against APC Requires significant compensation against RPE-Alexa Fluor 700 and APC-Alexa Fluor 750 Energy transfer dye excited at 633/635 nm with emission maximum at 775 nm Significantly more photostable than APC-Cy 7 Lower compensation when paired with APC than is needed with the APC-Cy 7/APC pair Brighter and more stabile than APC-Cy 7 Perfectly interchangeable with APC-Cy 7 due to spectral similarity between Alexa Fluor 750 dye and Cy 7 5
8 Flow Cytometry Fluorophore selection guide Instrument: Accuri C6 Flow Cytometer System Argon 488 FL1 Green 530/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 FL2 Yellow 585/ RPE PI Alexa Fluor 546 YO-PRO -1 phrodo dye Argon 488 FL3 Red 675LP 675 RPE-Alexa Fluor 700 PI TRI-COLOR RPE-Cy 7 RPE-Alexa Fluor 750 PerCP 7-AAD SNARF (high ph) He Ne 640 FL4 Red 675/ APC Click-iT EdU Alexa Fluor 647 Bold = recommended fluorophore. Alexa Fluor 647 Qdot 655 nanocrystal LIVE/DEAD Fixable Far Red Dead Cell Stain TO-PRO -3 SYTOX Red MitoProbe DiIC 1 (5) CellTrace Far Red DDAO-SE 6
9 Fluorophore selection guide Instrument: BD FACSCalibur System Argon 488 FL1 Green 530/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 FL2 Yellow 585/ RPE PI Alexa Fluor 546 YO-PRO -1 phrodo dye Argon 488 FL3 Red 670LP 670 RPE-Alexa Fluor 700 PI TRI-COLOR RPE-Cy 7 RPE-Alexa Fluor 750 PerCP 7-AAD SNARF (high ph) He Ne 635 FL4 Red 661/ APC Click-iT EdU Alexa Fluor 647 Bold = recommended fluorophore. Alexa Fluor 647 Qdot 655 nanocrystal LIVE/DEAD Fixable Far Red Dead Cell Stain TO-PRO -3 SYTOX Red MitoProbe DiIC 1 (5) CellTrace Far Red DDAO-SE 7
10 Flow Cytometry Fluorophore selection guide Instrument: BD FACScan Flow Cytometer Argon 488 FL1 Green 530/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 FL2 Yellow 585/ RPE PI Alexa Fluor 546 YO-PRO -1 phrodo dye Argon 488 FL3 Red 650LP 650 RPE-Alexa Fluor 700 PI Bold = recommended fluorophore. Qdot 655 nanocrystal TRI-COLOR RPE-Cy 7 RPE-Alexa Fluor 750 PerCP 7-AAD SNARF (high ph) 8
11 Fluorophore selection guide Instrument: BD FACSCanto System Argon 488 Green 530/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 Yellow 585/ RPE PI Alexa Fluor 546 YO-PRO -1 phrodo dye Argon 488 Red 670LP 670 RPE-Alexa Fluor 700 PI (695/40)* 7-AAD TRI-COLOR PerCP Argon 488 Infrared 780/ RPE-Cy 7 RPE-Alexa Fluor 750 (787/42)* SNARF (high ph) continued 9
12 Flow Cytometry Fluorophore selection guide Instrument: BD FACSCanto System, continued He Ne 633 Red 660/ APC Click-iT EdU Alexa Fluor 647 Alexa Fluor 647 Qdot 655 nanocrystal LIVE/DEAD Fixable Far Red Dead Cell Stain TO-PRO -3 SYTOX Red MitoProbe DiIC 1 (5) CellTrace Far Red DDAO-SE He Ne 633 Infrared 780/ APC-Alexa Fluor 750 LIVE/DEAD Fixable Near-IR Dead Cell Stain (787/42)* APC-Cy 7 10
13 Fluorophore selection guide Instrument: BD FACSCanto II System, 2- option Argon 488 Green 530/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 Yellow 585/ RPE PI Alexa Fluor 546 YO-PRO -1 phrodo dye Argon 488 Orange 616/ RPE-Alexa Fluor 610 PI RPE-Texas Red Argon 488 Red 670LP 670 RPE-Alexa Fluor 700 PI (695/40)* 7-AAD TRI-COLOR PerCP Argon 488 Infrared 780/ RPE-Cy 7 RPE-Alexa Fluor 750 (787/42)* SNARF (high ph) continued 11
14 Flow Cytometry Fluorophore selection guide Instrument: BD FACSCanto II System, 2- option, continued He Ne 633 Red 660/ APC Click-iT EdU Alexa Fluor 647 Alexa Fluor 647 Qdot 655 nanocrystal He Ne 633 Far Red 712/ Alexa Fluor 700 LIVE/DEAD Fixable Far Red Dead Cell Stain TO-PRO -3 SYTOX Red MitoProbe DiIC 1 (5) CellTrace Far Red DDAO-SE He Ne 633 Infrared 780/ APC-Alexa Fluor 750 LIVE/DEAD Fixable Near-IR Dead Cell Stain Available on some models. (787/42)* APC-Cy 7 12
15 Fluorophore selection guide Instrument: BD FACSCanto II System, 3- option Argon 488 Green 530/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 Yellow 585/ RPE PI Alexa Fluor 546 YO-PRO -1 phrodo dye Argon 488 Red 670LP 670 RPE-Alexa Fluor 700 PI (695/40)* 7-AAD TRI-COLOR PerCP Argon 488 Infrared 780/ RPE-Cy 7 RPE-Alexa Fluor 750 (787/42)* SNARF (high ph) 13
16 Flow Cytometry Fluorophore selection guide Instrument: BD FACSCanto II System, 3- option, continued He Ne 633 Red 660/ APC Click-iT EdU Alexa Fluor 647 Alexa Fluor 647 Qdot 655 nanocrystal LIVE/DEAD Fixable Far Red Dead Cell Stain TO-PRO -3 SYTOX Red MitoProbe DiIC 1 (5) CellTrace Far Red DDAO-SE He Ne 633 Infrared 780/ APC-Alexa Fluor 750 LIVE/DEAD Fixable Near-IR Dead Cell Stain (787/42)* APC-Cy 7 Violet 405 Blue 450/ Pacific Blue Click-iT EdU Pacific Blue Alexa Fluor 405 PO-PRO -1 DyeCycle Violet LIVE/DEAD Fixable Violet Dead Cell Stain Calcein Violet Violet 405 Green 513/ Qdot 525 nanocrystal SYTOX Blue Available on some models. AmCyan LIVE/DEAD Fixable Aqua Dead Cell Stain 14
17 Fluorophore selection guide Instrument: BD LSR Flow Cytometer Argon 488 Green 530/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 Yellow 585/ RPE PI Alexa Fluor 546 YO-PRO -1 phrodo dye Argon 488 Red 670LP 670 RPE-Alexa Fluor 700 PI (695/40)* 7-AAD TRI-COLOR PerCP Argon 488 Infrared 780/ RPE-Cy 7 RPE-Alexa Fluor 750 (787/42)* SNARF (high ph) continued 15
18 Flow Cytometry Fluorophore selection guide Instrument: BD LSR Flow Cytometer, continued He Cd 325 FL4 Violet 405/ Alexa Fluor 350 Indo-1 (high Ca 2+ ) He Cd 325 FL5 Blue 450/ DAPI Hoechst Calcein Blue SYTOX Blue LIVE/DEAD Fixable Blue Dead Cell Stain He Cd 325 Green 530/ Qdot 525 nanocrystal Indo-1 (low Ca 2+ ) SYTOX Blue He Ne 633 FL6 Red 660/ APC Click-iT EdU Alexa Fluor 647 Bold = recommended fluorophore. Alexa Fluor 647 Qdot 655 nanocrystal LIVE/DEAD Fixable Far Red Dead Cell Stain TO-PRO -3 CellTrace Far Red DDAO-SE SYTOX Red MitoProbe DiIC 1 (5) LIVE/DEAD Fixable Near-IR Dead Cell Stain 16
19 Fluorophore selection guide Instrument: BD LSR II Flow Cytometer Argon 488 Green 530/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 YO-PRO -1 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 Yellow 575/ RPE PI Alexa Fluor 546 phrodo dye Argon 488 Orange 610/ RPE-Alexa Fluor 610 PI RPE-Texas Red Qdot 605 nanocrystal Argon 488 Red 695/ RPE-Alexa Fluor 700 PI TRI-COLOR (670/14)* PerCP Argon 488 Infrared 780/ RPE-Cy 7 RPE-Alexa Fluor 750 (787/42)* 7-AAD SNARF (high ph) continued 17
20 Flow Cytometry Fluorophore selection guide Instrument: BD LSR II Flow Cytometer, continued He Ne 633 Red 660/ APC Click-iT EdU Alexa Fluor 647 Alexa Fluor 647 Qdot 655 nanocrystal He Ne 633 Red 710/ Alexa Fluor 700 LIVE/DEAD Fixable Far Red Dead Cell Stain TO-PRO -3 SYTOX Red MitoProbe DiIC 1 (5) CellTrace Far Red DDAO-SE He Ne 633 Infrared 780/ APC-Alexa Fluor 750 (787/42)* LIVE/DEAD Fixable Near-IR Dead Cell Stain APC-Cy 7 UV 355 Violet 405/ Alexa Fluor 350 Indo-1 (high Ca 2+ ) UV 355 Blue 450/ Hoechst DAPI Calcein Blue LIVE/DEAD Fixable Blue Dead Cell Stain UV 355 Green 530/ Qdot 525 nanocrystal Indo-1 (low Ca 2+ ) Violet 405 Blue 440/ Pacific Blue Click-iT EdU Pacific Blue Alexa Fluor 405 PO-PRO -1 DyeCycle Violet LIVE/DEAD Fixable Violet Dead Cell Stain Calcein Violet Violet 405 Green 525/ Qdot 525 nanocrystal (525/20)* SYTOX Blue AmCyan Violet 405 Yellow 585/ Pacific Orange (565/20)* (585/20)* Violet 405 Orange 610/ Qdot 605 nanocrystal Violet 405 Red 655/ Qdot 655 nanocrystal Violet 405 Red 720/ Violet 405 Infrared 787/ Available on some models. LIVE/DEAD Fixable Aqua Dead Cell Stain 18
21 Fluorophore selection guide Instrument: BD FACSAria Cell Sorter Argon 488 Green 530/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 Yellow 575/ RPE PI Alexa Fluor 546 YO-PRO -1 phrodo dye Argon 488 Red 610/ RPE-Alexa Fluor 610 PI RPE-Texas Red Qdot 605 nanocrystal Argon 488 Far Red 695/ RPE-Alexa Fluor AAD TRI-COLOR PerCP Argon 488 Infrared 780/ RPE-Cy 7 RPE-Alexa Fluor 750 (787/42)* SNARF (high ph) continued 19
22 Flow Cytometry Fluorophore selection guide Instrument: BD FACSAria Cell Sorter, continued He Ne 633 Red 660/ APC Click-iT EdU Alexa Fluor 647 Alexa Fluor 647 Qdot 655 nanocrystal He Ne 633 Infrared 780/ APC-Alexa Fluor 750 (787/42)* APC-Cy 7 LIVE/DEAD Fixable Far Red Dead Cell Stain TO-PRO -3 SYTOX Red MitoProbe DiIC 1 (5) CellTrace Far Red DDAO-SE LIVE/DEAD Fixable Near-IR Dead Cell Stain Violet 407 Blue 450/ Pacific Blue Click-iT EdU Pacific Blue Alexa Fluor 405 LIVE/DEAD Fixable Violet Dead Cell Stain PO-PRO -1 DyeCycle Violet Calcein Violet Violet 407 Green 530/ Qdot 525 nanocrystal LIVE/DEAD Fixable Aqua Dead Cell Stain AmCyan Violet 407 Yellow 585/ Pacific Orange (565/20)* (585/20)* Violet 407 Orange 610/ Qdot 605 nanocrystal Violet 407 Red 655/ Qdot 655 nanocrystal Violet 407 Red 720/ Violet 407 Infrared 787/ SYTOX Blue 20
23 Fluorophore selection guide Instrument: BD FACSArray Bioanalyzer System channel Possible filters Filter range (nm) Fluorophores Other fluorescent dyes Green He Ne 532 Yellow 585/ RPE PI Alexa Fluor 546 Alexa Fluor 568 phrodo dye Green He Ne 532 Red 685LP 685 RPE-Alexa Fluor 700 PI TRI-COLOR (670/14)* RPE-Alexa Fluor 750 RPE-Cy 7 7-AAD SNARF (high ph) He Ne 633 Red 661/ APC Click-iT EdU Alexa Fluor 647 Alexa Fluor 647 Qdot 655 nanocrystal LIVE/DEAD Fixable Far Red Dead Cell Stain TO-PRO -3 SYTOX Red MitoProbe DiIC 1 (5) CellTrace Far Red DDAO-SE He Ne 633 Infrared 788/ APC-Alexa Fluor 750 LIVE/DEAD Fixable Near-IR Dead Cell Stain APC-Cy
24 Flow Cytometry Fluorophore selection guide Instrument: BD FACSVantage SE Cell Sorter channel Possible filters Filter range (nm) Fluorophores Other fluorescent dyes Argon 488 Green 530/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 Yellow 575/ RPE PI Alexa Fluor 546 YO-PRO -1 phrodo dye Argon 488 Orange 610/ RPE-Alexa Fluor 610 PI RPE-Texas Red Qdot 605 nanocrystal Argon 488 Red 700/ RPE-Alexa Fluor 700 (695/40)* PI TRI-COLOR (670/14)* Argon 488 Infrared 780/ RPE-Cy 7 RPE-Alexa Fluor 750 (787/42)* 7-AAD SNARF (high ph) 22
25 Fluorophore selection guide Instrument: BD FACSVantage SE Cell Sorter, continued channel Possible filters Filter range (nm) Fluorophores Other fluorescent dyes He Ne 633 Red 660/ APC Click-iT EdU Alexa Fluor 647 Alexa Fluor 647 Qdot 655 nanocrystal He Ne 633 Red 710/ Alexa Fluor 700 LIVE/DEAD Fixable Far Red Dead Cell Stain TO-PRO -3 SYTOX Red MitoProbe DiIC 1 (5) CellTrace Far Red DDAO-SE He Ne 633 Infrared 780/ APC-Alexa Fluor 750 LIVE/DEAD Fixable Near-IR Dead Cell Stain (787/42)* APC-Cy 7 UV 355 Violet Indo-1 (high Ca 2+ ) UV 355 Blue 424/ Alexa Fluor 350 DAPI Hoechst Calcein Blue LIVE/DEAD Fixable Blue Dead Cell Stain UV 355 Green 530/ Qdot 525 nanocrystal Indo-1 (low Ca 2+ ) UV 355 Blue 440/ Pacific Blue Click-iT EdU Pacific Blue Alexa Fluor 405 PO-PRO -1 DyeCycle Violet LIVE/DEAD Fixable Violet Dead Cell Stain UV 355 Green 530/ Qdot 525 nanocrystal SYTOX Blue AmCyan UV 355 Yellow 575/ Pacific Orange (565/20)* (585/20)* UV 355 Orange 610/ Qdot 605 nanocrystal UV 355 Red 655/ Qdot 655 nanocrystal UV 355 Red 720/ UV 355 Infrared 787/ LIVE/DEAD Fixable Aqua Dead Cell Stain continued 23
26 Flow Cytometry Fluorophore selection guide Instrument: BD FACSVantage SE Cell Sorter, continued channel Possible filters Filter range (nm) Fluorophores Other fluorescent dyes Green He Ne 532 Yellow 575/ RPE PI Alexa Fluor 546 Alexa Fluor 568 Green He Ne 532 Orange 610/ RPE-Alexa Fluor 610 RPE-Texas Red phrodo dye Green He Ne 532 Red 695/ RPE-Alexa Fluor 700 PI TRI-COLOR (670/14)* Green He Ne 532 Infrared 780/ RPE-Cy 7 RPE-Alexa Fluor 750 (787/42)* 7-AAD SNARF (high ph) 24
27 Fluorophore selection guide Instrument: Beckman Coulter Cytomics FC 500 Flow Cytometer Argon 488 Green 525BP Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 Yellow 575BP RPE PI Alexa Fluor 546 YO-PRO -1 phrodo dye Argon 488 Orange 620BP RPE-Alexa Fluor 610 PI RPE-Texas Red Qdot 605 nanocrystal Argon 488 Red 675/ RPE-Alexa Fluor 700 (710/20)* TRI-COLOR (670/14)* PerCP Argon 488 Red 755/ RPE-Alexa Fluor 750 (787/42)* RPE-Cy 7 PI 7-AAD SNARF (high ph) continued 25
28 Flow Cytometry Fluorophore selection guide Instrument: Beckman Coulter Cytomics FC 500 Flow Cytometer, continued He Ne 633 Red 675/ APC Click-iT EdU Alexa Fluor 647 Alexa Fluor 647 Alexa Fluor 700 (710/20)* LIVE/DEAD Fixable Far Red Dead Cell Stain TO-PRO -3 CellTrace Far Red DDAO-SE MitoProbe DiIC 1 (5) SYTOX Red He Ne 633 Infrared 755/ APC-Alexa Fluor 750 (787/42)* LIVE/DEAD Fixable Near-IR Dead Cell Stain APC-Cy 7 26
29 Fluorophore selection guide Instrument: Beckman Coulter EPICS XL Flow Cytometer Argon 488 Green 525/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 Yellow 575/ RPE PI Alexa Fluor 546 YO-PRO -1 phrodo dye Argon 488 Orange 620/ RPE-Alexa Fluor 610 PI RPE-Texas Red Qdot 605 nanocrystal Argon 488 Red 675/ RPE-Alexa Fluor 700 (710/20)* PI TRI-COLOR (670/14)* PerCP 7-AAD SNARF (high ph) 27
30 Flow Cytometry Fluorophore selection guide Instrument: Beckman Coulter Cell Lab Quanta SC Argon 488 Green 525BP Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 Yellow 575BP RPE PI Alexa Fluor 546 YO-PRO -1 phrodo dye Argon 488 Red 670LP 670 RPE-Alexa Fluor 700 PI TRI-COLOR (670/14)* PerCP RPE-Cy 7 RPE-Alexa Fluor AAD 28
31 Fluorophore selection guide Instrument: Beckman Coulter Cell Lab Quanta SC, continued filter 355 Light source channel Default filter Fluorophores Other fluorescent dyes Mercury-arc Violet 405BP Alexa Fluor 350 Indo-1 (high Ca 2+ ) Mercury-arc Blue 450BP Hoechst DAPI Calcein Blue LIVE/DEAD Fixable Blue Dead Cell Stain Mercury-arc Green 525BP Qdot 525 nanocrystal Indo-1 (low Ca 2+ ) filter 405 Light source channel Default filter Fluorophores Other fluorescent dyes Mercury-arc Blue 440BP Pacific Blue Click-iT EdU Pacific Blue Alexa Fluor 405 PO-PRO -1 DyeCycle Violet LIVE/DEAD Fixable Violet Dead Cell Stain Calcein Violet Mercury-arc Green 525BP Qdot 525 nanocrystal (525/20)* SYTOX Blue AmCyan LIVE/DEAD Fixable Aqua Dead Cell Stain Mercury-arc Yellow 585BP Pacific Orange (565/20)* (585/20)* 29
32 Flow Cytometry Fluorophore selection guide Instrument: Beckman Coulter EPICS ALTRA Cell Sorter channel Possible filters Filter range (nm) Fluorophores Other fluorescent dyes Argon 488 Green 530/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 Yellow 575/ RPE PI Alexa Fluor 546 YO-PRO -1 phrodo dye Argon 488 Orange (610/20) RPE-Alexa Fluor 610 PI RPE-Texas Red Qdot 605 nanocrystal Argon 488 Red 695/ RPE-Alexa Fluor 700 PI TRI-COLOR (670/14)* PerCP Argon 488 Infrared 780/ RPE-Cy 7 RPE-Alexa Fluor 750 (787/42)* 7-AAD SNARF (high ph) 30
33 Fluorophore selection guide Instrument: Beckman Coulter EPICS ALTRA Cell Sorter, continued channel Possible filters Filter range (nm) Fluorophores Other fluorescent dyes He Ne 633 Red 660/ APC Click-iT EdU Alexa Fluor 647 Alexa Fluor 647 Qdot 655 nanocrystal LIVE/DEAD Fixable Far Red Dead Cell Stain TO-PRO -3 SYTOX Red MitoProbe DiIC 1 (5) CellTrace Far Red DDAO-SE He Ne 633 Red (710/20) Alexa Fluor 700 LIVE/DEAD Fixable Near-IR Dead Cell Stain He Ne 633 Infrared 780/ APC-Alexa Fluor 750 (787/42)* APC-Cy 7 UV 355 Violet 405/ Indo-1 (high Ca 2+ ) UV 355 Blue 450/ Alexa Fluor 350 DAPI Hoechst Calcein Blue UV 355 Green 530/ Qdot 535 nanocrystal Indo-1 (low Ca 2+ ) Violet 405 Blue 440/ Pacific Blue Click-iT EdU Pacific Blue Alexa Fluor 405 PO-PRO -1 DyeCycle Violet LIVE/DEAD Fixable Violet Dead Cell Stain Calcein Violet Violet 405 Green 530/ Qdot 525 nanocrystal SYTOX Blue AmCyan Violet 405 Yellow 575/ Pacific Orange (565/20)* (585/20)* LIVE/DEAD Fixable Aqua Dead Cell Stain continued 31
34 Flow Cytometry Fluorophore selection guide Instrument: Beckman Coulter EPICS ALTRA Cell Sorter, continued channel Possible filters Filter range (nm) Fluorophores Other fluorescent dyes Violet 405 Orange 610/ Qdot 605 nanocrystal Violet 405 Red 655/ Qdot 655 nanocrystal Violet 405 Red 720/ Violet 405 Infrared 787/ Green He Ne 532 Yellow 575/ RPE PI Alexa Fluor 546 Alexa Fluor 568 phrodo dye Green He Ne 532 Orange 610/ RPE-Alexa Fluor 610 PI RPE-Texas Red Qdot 605 nanocrystal Green He Ne 532 Red 695/ RPE-Alexa Fluor 700 PI TRI-COLOR (670/14)* Green He Ne 532 Infrared 780/ RPE-Cy 7 RPE-Alexa Fluor 750 (787/42)* 7-AAD SNARF (high ph) 32
35 Fluorophore selection guide Instrument: Beckman Coulter CyAn ADP Analyzer Argon 488 Green 530/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 Yellow 575/ RPE PI Alexa Fluor 546 YO-PRO -1 phrodo dye Argon 488 Orange 620/ RPE-Alexa Fluor 610 PI RPE-Texas Red Qdot 605 nanocrystal Argon 488 Red 680/ RPE-Alexa Fluor 700 (695/40)* PI TRI-COLOR (670/14)* PerCP Argon 488 Infrared 750LP 750 RPE-Cy 7 RPE-Alexa Fluor 750 (787/42)* 7-AAD SNARF (high ph) continued 33
36 Flow Cytometry Fluorophore selection guide Instrument: Beckman Coulter CyAn ADP Analyzer, continued He Ne 633 Red 665/ APC Click-iT EdU Alexa Fluor 647 Alexa Fluor 647 Qdot 655 nanocrystal He Ne 633 Red 670/ Alexa Fluor /40 Alexa Fluor 700 Qdot 655 nanocrystal LIVE/DEAD Fixable Far Red Dead Cell Stain TO-PRO -3 SYTOX Red MitoProbe DiIC 1 (5) CellTrace Far Red DDAO-SE He Ne 633 Infrared 750LP 750 APC-Alexa Fluor 750 (787/42)* LIVE/DEAD Fixable Near-IR Dead Cell Stain APC-Cy 7 Violet 405 Blue 450/ Pacific Blue Click-iT EdU Pacific Blue Alexa Fluor 405 PO-PRO -1 DyeCycle Violet LIVE/DEAD Fixable Violet Dead Cell Stain Calcein Violet Violet 405 Green 530/ Qdot 525 nanocrystal SYTOX Blue AmCyan Violet 405 Yellow 575/ Pacific Orange (565/20)* (585/20)* Violet 405 Orange 610/ Qdot 605 nanocrystal Violet 405 Red 655/ Qdot 655 nanocrystal Violet 405 Red 720/ Violet 405 Infrared 787/ LIVE/DEAD Fixable Aqua Dead Cell Stain 34
37 Fluorophore selection guide Instrument: Beckman Coulter MoFlo XDP Cell Sorter Argon 488 Green 530/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 Yellow 575/ RPE PI Alexa Fluor 546 YO-PRO -1 phrodo dye Argon 488 Orange 610/ RPE-Alexa Fluor 610 PI RPE-Texas Red Qdot 605 nanocrystal Argon 488 Red 700/ RPE-Alexa Fluor 700 (695/40)* PI TRI-COLOR (670/14)* Argon 488 Infrared 780/ RPE-Cy 7 RPE-Alexa Fluor 750 (787/42)* 7-AAD SNARF (high ph) continued 35
38 Flow Cytometry Fluorophore selection guide Instrument: Beckman Coulter MoFlo XDP Cell Sorter, continued channel Default filter Filter range (nm) Fluorophores Other fluorescent dyes HeNe 633 Red 660/ APC TO-PRO -3 Alexa Fluor 647 Qdot 655 nanocrystal HeNe 633 Red (710/20) Alexa Fluor 700 SYTOX Red LIVE/DEAD Fixable Far Red Dead Cell Stain Click-iT EdU Alexa Fluor 647 MitoProbe DiIC 1 (5) CellTrace Far Red DDAO-SE HeNe 633 Infrared 780/ APC-Alexa Fluor 750 (787/42)* LIVE/DEAD Fixable Near-IR Dead Cell Stain APC-Cy 7 HeNe 633 Violet Indo-1 (High Ca 2+ ) HeNe 633 Blue 424/ Alexa Fluor 350 DAPI Hoechst Calcein Blue LIVE/DEAD Fixable Blue Dead Cell Stain Calcein Violet HeNe 633 Green 530/ Qdot 525 nanocrystal Indo-1 (Low Ca 2+ ) Violet 405 Blue 440/ Pacific Blue PO-PRO -1 Alexa Fluor 405 DyeCycle Violet Click-iT EdU Pacific Blue LIVE/DEAD Fixable Violet Dead Cell Stain Calcein Violet Violet 405 Green 530/ Qdot 525 nanocrystal SYTOX Blue AmCyan Violet 405 Yellow 575/ Pacific Orange (565/20)* (585/20)* Violet 405 Orange (610/20) Qdot 605 nanocrystal Violet 405 Red (655/20) Qdot 655 nanocrystal Violet 405 Red (720/40) Violet 405 Infrared (787/42) LIVE/DEAD Fixable Aqua Dead Cell Stain 36
39 Fluorophore selection guide Instrument: Beckman Coulter MoFlo XDP Cell Sorter, continued Green HeNe 532 Yellow 575/ RPE PI Alexa Fluor 546 Alexa Fluor 568 Green HeNe 532 Orange (610/20) RPE-Alexa Fluor 610 PI RPE-Texas Red Qdot 605 nanocrystal Green HeNe 532 Red 695/ RPE-Alexa Fluor 700 PI TRI-COLOR (670/14)* Green HeNe 532 Infrared 780/ RPE-Cy 7 RPE-Alexa Fluor 750 (787/42)* 7-AAD SNARF (high ph) 37
40 Flow Cytometry Fluorophore selection guide Instrument: Guava Personal Cell Analysis (PCA) System He Ne 532 Green 580/ RPE PI phrodo dye He Ne 532 Red 675/ PI Bold = recommended fluorophore. TRI-COLOR 7-AAD 38
41 Fluorophore selection guide Instrument: Guava EasyCyte Mini System Argon 488 Green 525/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 Yellow 583/ RPE PI Alexa Fluor 546 Alexa Fluor 568 YO-PRO -1 phrodo dye Argon 488 Red 680/ RPE-Alexa Fluor 700 PI Bold = recommended fluorophore. TRI-COLOR 7-AAD SNARF (high ph) 39
42 Flow Cytometry Fluorophore selection guide Instrument: Guava EasyCyte Plus System Argon 488 Green 525/ Alexa Fluor 488 Click-iT EdU Alexa Fluor 488 Fluorescein Qdot 525 nanocrystal Calcein Fluo-3 or Fluo-4 TO-PRO -1 CFSE GFP SYTOX Green DyeCycle Green Rhodamine 123 LIVE/DEAD Fixable Green Dead Cell Stain Argon 488 Yellow 583/ RPE PI Alexa Fluor 546 Alexa Fluor 568 YO-PRO -1 phrodo dye Argon 488 Red 680/ RPE-Alexa Fluor 700 PI TRI-COLOR Argon 488 Red 755/ RPE-Cy 7 Bold = recommended fluorophore. RPE-Alexa Fluor 750 s 7-AAD SNARF (high ph) 40
43 Index Name used on instrument pages Catalog number Formal name 7-AAD A aminoactinomycin D (7-AAD) Calcein * C3100MP calcein, AM *special packaging* Calcein Blue C34853 CellTrace calcein blue, AM *special packaging* Calcein Violet C34858 CellTrace calcein violet, AM *for 405 nm excitation* *special packaging* CellTrace Far Red DDAO-SE C34553 CellTrace Far Red DDAO-SE *special packaging* CFSE C34554 CellTrace CFSE Cell Proliferation Kit *for flow cytometry* Click-iT EdU Alexa Fluor 488 C35002 Click-iT EdU Alexa Fluor 488 Flow Cytometry Assay Kit *50 assays* Click-iT EdU Alexa Fluor 647 A10202 Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay Kit *50 assays* Click-iT EdU Pacific Blue A10034 Click-iT EdU Pacific Blue Flow Cytometry Assay Kit *50 assays* DAPI * D3571 4,6-diamidino-2-phenylindole, dilactate (DAPI, dilactate) DyeCycle Green V35004 Vybrant DyeCycle Green stain *5 mm solution in DMSO* *200 assays* V35005 Vybrant stain *5 mm solution in DMSO* *200 assays* DyeCycle Violet V35003 Vybrant DyeCycle Violet stain *5 mm in water* *200 assays* DiOC 2 (3) M34150 MitoProbe DiOC 2 (3) Assay Kit *for flow cytometry* *100 assays* Fluo-3 * F1242 fluo-3, AM *cell permeant* *special packaging* Fluo-4 * F14201 fluo-4, AM *cell permeant* *special packaging* * F3021, AM *cell permeant* *special packaging* Hoechst H3570 Hoechst 33342, trihydrochloride, trihydrate *10 mg/ml solution in water* Indo-1 * I1223 indo-1, AM *cell permeant* *special packaging* JC-1 M34152 MitoProbe JC-1 Assay Kit *for flow cytometry* *100 assays* LIVE/DEAD Fixable Aqua Dead Cell Stain L34957 LIVE/DEAD Fixable Aqua Dead Cell Stain Kit *for 405 nm excitation* *200 assays* LIVE/DEAD Fixable Blue Dead Cell Stain L23105 LIVE/DEAD Fixable Blue Dead Cell Stain Kit *for flow cytometry* *200 assays* LIVE/DEAD Fixable Far Red Dead Cell Stain L10120 LIVE/DEAD Fixable Far Red Dead Cell Stain Kit *for 633 or 635 nm excitation* *200 assays* LIVE/DEAD Fixable Green Dead Cell Stain L23101 LIVE/DEAD Fixable Green Dead Cell Stain Kit *for flow cytometry* *200 assays* LIVE/DEAD Fixable Near-IR Dead Cell Stain L10119 LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit *for 633 or 635 nm excitation* *200 assays* L23102 Kit *for flow cytometry* *200 assays* LIVE/DEAD Fixable Violet Dead Cell Stain L34955 LIVE/DEAD Fixable Violet Dead Cell Stain Kit *for flow cytometry* *200 assays* MitoProbe DilC1(5) M34151 MitoProbe DiIC1(5) Assay Kit *for flow cytometry* *100 assays* phrodo dye * A10025 phrodo E. coli BioParticles Phagocytosis Kit *for flow cytometry* *100 tests* PI P3566 propidium iodide *1.0 mg/ml solution in water* PO-PRO -1 P3581 PO-PRO -1 iodide (435/455) *1 mm solution in DMSO* Rhodamine 123 R302 rhodamine 123 SNARF S22801 SNARF -1 carboxylic acid, acetate, succinimidyl ester *special packaging* SYTOX Blue * S34857 SYTOX Blue dead cell stain *for flow cytometry* *1000 assays* *1 mm solution in DMSO* SYTOX Green S7020 SYTOX Green nucleic acid stain *5 mm solution in DMSO* SYTOX Red S34859 SYTOX Red dead cell stain *for 633 or 635 nm excitation* *5 µm solution in DMSO* TO-PRO -1 T3602 TO-PRO -1 iodide (515/531) *1 mm solution in DMSO* TO-PRO -3 T3605 TO-PRO -3 iodide (642/661) *1 mm solution in DMSO* YO-PRO -1 Y3603 YO-PRO -1 iodide (491/509) *1 mm solution in DMSO* * Other packaging formats available. 41
44 Flow Cytometry Trademarks of other companies referred to in this fluorophore selection guide include: Accuri C6 Flow Cytometer (Accuri, Inc.) BD (Becton, Dickinson and Company) CyAn (Beckman Coulter, Inc.) EasyCyte (Guava Technologies, Inc.) EPICS ALTRA (Beckman Coulter, Inc.) BD FACSAria (Becton, Dickinson and Company) BC FACSArray (Becton, Dickinson and Company) BD FACSCalibur (Becton, Dickinson and Company) BD FACScan (Becton, Dickinson and Company) BD FACSCanto (Becton, Dickinson and Company) BD FACSVantage SE (Becton, Dickinson and Company EPICS XL (Beckman Coulter, Inc.) Guava (Guava Technologies, Inc.) Guava EasyCyte (Guava Technologies, Inc.) MoFlo (Beckman Coulter, Inc.) Quanta (Beckman Coulter, Inc.) 42
45 2007 Invitrogen Corporation. All rights reserved. These products may be covered by one or more Limited Use Label Licenses (see Invitrogen catalog or By use of these products you accept the terms and conditions of all applicable Limited Use Label Licenses. For research use only. Not intended for any animal or human therapeutic or diagnostic use, unless otherwise stated. O r
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Pantone Matching System Color Chart PMS Colors Used For Printing Use this guide to assist your color selection and specification process. This chart is a reference guide only. Pantone colors on computer
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