As shown in Figure T13.7, the Gate Navigator is organized by the gates used in the layout. Under each gate, is the list of the plots gated on this gate.  As you move the cursor over the plots listed in the Gate Navigator, thumbprint images of the plots appear. This is a helpful quick reminder of which plot is gated on a gate, and is particularly useful if that plot is not currently visible.

We will now explore the features of the Gate Navigator, beginning with applying a gate to a plot on the layout using the Gate Navigator. Specifically, we will apply the CD3 gate and then the FL2+ gate to 2D plots on the layout.

1.Place the cursor over the CD3 gate in the Gate Navigator, highlighted in blue in Figure T13.8.
2.Press and hold the left mouse button.
3.Drag the CD3 gate onto the layout.
4.Release the mouse button when the CD3 gate is on top of the 2D density plot of CD3-FITC (FITC fluorescence vs. SSC-H) in the second row of the left column of the layout, outlined in blue and indicated by the cursor in Figure T13.8.

 

Figure T13.8  Dragging and Dropping the CD3 Gate from the Gate Navigator onto a Density Plot on the Layout

Figure T13.8  Dragging and Dropping the CD3 Gate from the Gate Navigator onto a Density Plot on the Layout

 

The 2D density plot of CD3-FITC (FITC vs. SSC-H) will now update to reflect that is gated on the CD3 gate, as shown in Figure T13.9. The Gate Navigator also updates, and under the CD3 gate is a new listing for the 2D density plot CD3-FITC (FL1-H vs. SSC-H), indicated by the cursor and the thumbnail image in Figure T13.9.

 

Figure T13.9  Application of the CD3 Gate to the 2D Density Plot of CD3-FITC (FL1-H vs. SSC-H)

Figure T13.9  Application of the CD3 Gate to the 2D Density Plot of CD3-FITC (FL1-H vs. SSC-H)

 

We will now use drag and drop to apply the CD3 gate from the Gate Navigator to the other FITC Fluorescence vs. SSC-H 2D plots on the layout.

5.Repeat steps 1 through 3.
6.Release the left mouse button when the CD3 gate is on top of the 2D density plot of CD4-PE (FITC fluorescence vs. SSC-H), located in the second row of the middle column of the layout.

Both the 2D plot and the Gate Navigator update to reflect the application of the CD3 gate to the CD4-PE (FITC fluorescence vs. SSC-H) plot, as shown in Figure T13.10.

 

Figure T13.10  Application of the CD3 Gate to the 2D Density Plot of CD4-PE (FL1-H vs. SSC-H)

Figure T13.10  Application of the CD3 Gate to the 2D Density Plot of CD4-PE (FL1-H vs. SSC-H)

 

7.Repeat steps 1 through 3.
8.Release the left mouse button when the CD3 gate is on top of the 2D density plot of CD3-FITC+CD4-PE (FITC fluorescence vs. SSC-H), located in the second row of the last column of the layout.

Both the 2D plot and the Gate Navigator update to reflect the application of the CD3 gate to the CD3-FITC+CD4-PE (FITC fluorescence vs. SSC-H) plot, as shown in Figure T13.11.

 

Figure T13.11  Application of the CD3 Gate to the 2D Density Plot of CD3-FITC+CD4-PE (FL1-H vs. SSC-H)

Figure T13.11  Application of the CD3 Gate to the 2D Density Plot of CD3-FITC+CD4-PE (FL1-H vs. SSC-H)

 

We will now apply the FL2+ gate to the 2D plots of PE Fluorescence vs. SSC-H in the third row of the layout.

9. Place the cursor over the FL2+ gate in the Gate Navigator.
10. Press and hold the left mouse button.
11. Drag the FL2+ gate onto the layout.
12. Release the mouse button when the FL2+ gate is on top of the 2D density plot of CD3-FITC (PE fluorescence vs. SSC-H), located in the third row of the first column of the layout.

Both the 2D plot and the Gate Navigator update to reflect the application of the FL2+ gate to the CD3-FITC (PE Fluorescence vs. SSC-H) plot. We will now apply the FL2+ gate to the other 2D plots of PE Fluorescence vs. SSC-H).

13. Repeat steps 9 through 11.
14. Release the mouse button when the FL2+ gate is on top of the 2D density plot of CD4-PE (PE fluorescence vs. SSC-H), located in the third row of the middle column of the layout.
15. Repeat steps 9 through 11.
16. Release the mouse button when the FL2+ gate is on top of the 2D density plot of CD3-FITC+CD4-PE (PE fluorescence vs. SSC-H), located in the third row of the right column of the layout.

The 2D plots on the layout and Gate Navigator should now look similar to Figure T13.12.

 

Figure T13.12  2D Plots and Gate Navigator Updated to Reflect the Application of Gates

Figure T13.12  2D Plots and Gate Navigator Updated to Reflect the Application of Gates

 

Now that we have lots of 2D plots using gates, we can drag and drop gates on the Gate Navigator itself to change how plots are gated. We will now apply the Lymphs gate to a 2D plot that is currently being gated on the CD3 gate using only the Gate Navigator.

17. Place the cursor on the Lymphs gate, shown highlighted in blue in Figure T13.13.
18. Press and hold the left mouse button.
19. Drag the Lymphs gate down the Gate Navigator.
20. Release the mouse button when the Lymphs gate is on top of the listing for 2 - Density – CD3 FITC.002 compensated (FL1-H vs. SSC-H), indicated by the cursor and highlighted in blue in Figure T13.13.

 

Figure T13.13  Dragging and Dropping the Lymphs Gate on the Gate Navigator

Figure T13.13  Dragging and Dropping the Lymphs Gate on the Gate Navigator

 

The Lymphs gate has now been applied to the 2D plot of the CD3-FITC.002 (FL1-H vs. SSC-H) by simply dragging and dropping the gate on the Gate Navigator. The updated 2D plot is shown highlighted in green, and the updated Gate Navigator listing of the plot is indicated by the cursor and the thumbnail image in Figure T13.14.

 

Figure T13.14  Updated Gate Navigator and Layout Reflect the Application of the Lymphs Gate

Figure T13.14  Updated Gate Navigator and Layout Reflect the Application of the Lymphs Gate

 

Instead of dragging and dropping the Lymphs gate onto the plot, we could have used the associated pop-up menu.

 

We will now use the Gate Navigator to move a plot onto a new page in the layout. First, we will insert a new page on the layout.

 

21. Click on the insert new Page icon, located on the bottom border of the layout, indicated by the cursor in Figure T13.15.

 

Figure T13.15  Insert New Page

Figure T13.15  Insert New Page

 

Alternatively, you can insert a new Page using the Insert command.

 

•Select the Insert→General→New Page command, indicated by the cursor in Figure T13.16.

 

Figure T13.16  Selecting the Insert New Page Command

Figure T13.16  Selecting the Insert New Page Command

 

A new blank page appears on the layout.

22. Place the cursor over the listing for 2D density plot CD3FITC.002 (FL1-H vs. FL2-H) listed under the Lymphs gate on the Data Navigator, shown highlighted in blue in Figure T13.17.
23. Press and hold the left mouse button.
24. Continue to hold down the mouse button and drag the plot listing from the Gate Navigator onto page 2 of the layout.
25. Release the mouse button when the plot listing is on page 2, indicated by the cursor in Figure T13.17.

 

Figure T13.17  Dragging and Dropping a 2D Density Plot Listing onto Page 2 of the Layout

Figure T13.17  Dragging and Dropping a 2D Density Plot Listing onto Page 2 of the Layout

 

A new density plot, 18 - CD3FITC.002 compensated (FL1-H vs. FL2-H), appears under the Lymphs gate and on the new page of the layout, similar to Figure T13.18.

 

 

Figure T13.18  2D Plot on Page 2 of the Layout

Figure T13.18  2D Plot on Page 2 of the Layout

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