====== Creating the PCR Plate ======


The extracted DNA is transferred to the PCR plate in exactly the same arrangement, i.e. the samples remain in the same wells. For creating a PCR plate, use the search function and find the extraction plate and mark it:

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Click again on **New Reaction** in the navigation bar. This time set **Type of reaction = PCR** in the pop-up window and make sure that **Create plate from existing documents** is selected so that the sample IDs are taken over from the extraction plate.

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A view of the PCR plate opens: first of all enter the **plate name** in the format ''CaBOL_PCR_xxxx''. The plate number is the same as that of the extraction plate.

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Now the **Lab information** can be stored like we did before for the extraction plate: Select the used PCR program under **Thermocycle**.

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Click on **Edit All Wells** to open a new window:

Select ''Locus'' and enter the ''Date'', the ''Primer'' used and the ''Technician''. The primer sequences are available in the **Shared database** in the folder **Primer**.

:!: Press **OK** to close the **Edit Wells** window and return to the plate view :!:.

===== Attach Gel Image: =====

Click on** Attach GEL Image** to open a new window where a gel image can be inserted.

Click on **Add** to select the corresponding gel image from the storing location.

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Via **Split GEL** the plate positions are mapped onto the gel image.

Enter the ''number of rows'' and ''columns'' and the ''starting position'' and draw a frame around the place on the gel image that belongs to each well. In this example, it is done row by row. Use the **Toggle Direction** button if the well number in the frame is not according to the well of the plate. Each time, press **OK** to return to the previous **Edit Gel Images** window.

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Based on the gel images, the **Reaction State** of the samples is automatically marked as **passed** (green) or **failed** (red). This classification can – and often should – be corrected manually by double clicking on the well because in some cases the automatic classification by the program seems to be a bit incomprehensible.

Based on my experience in this example I would definitely classify ''A1'', ''B9'', and ''E3'' promising gel signals (passed). There is also the option to set reactions on the state ''suspect'' what I would do for ''D12'' in this example. Select **Reaction State = run** for the negative control.

:!: Close the plate view with **OK** to save the new plate :!:.