Quantify DNA (Optional)

This step creates a Standard DNA plate with serial dilutions of stock Lambda DNA in the wells of column 1.

1.

Add stock Lambda DNA to well A1 in the Standard DNA plate and dilute to 75 ng/µl in a final volume of 233.3 µl. Pipette up and down several times to mix.

•

Use the following formula to calculate the amount of stock Lambda DNA:

•

Dilute the stock DNA in well A1 using the following formula:

2.

Add 66.7 µl 1X TE to well B1.

3.

Add 100 µl 1X TE to the remaining wells of column 1.

4.

Transfer 133.3 µl Lambda DNA from well A1 to well B1. Pipette up and down several times to mix.

5.

Transfer 100 µl from well B1 to well C1. Pipette up and down several times to mix.

6.

Repeat the sequential transfer of 100 µl for wells D1, E1, F1, and G1.

Do not transfer from well G1 to H1. Well H1 serves as the blank 0 ng/µl Lambda DNA.

7.

Cover the Standard DNA plate with a cap mat.

In this step, PicoGreen is diluted for use in the subsequent Create Standard and Sample QDNA Plates procedure.

1.

Prepare a 1:200 dilution of PicoGreen to 1X TE using a sealable 100 ml or 250 ml Nalgene bottle wrapped in aluminum foil.

Use the following table to determine the volumes needed for 96-well QDNA plates.

2.

Cap the foil-wrapped bottle and vortex to mix.

This step transfers the PicoGreen/1X TE dilution to Standard and Sample QDNA plates, and adds DNA from the respective DNA plates.

1.

At the robot PC, select DNA Quant, and then select Make Quant.

2.

Select the DNA plate type.

3.

In the Basic Run Parameters pane, enter the Number of DNA/QDNA plates (1, 2, or 3 pairs) and the Number of DNA Samples.

4.

Vortex DNA Sample plate at 1450 rpm for 1 minute.

5.

Centrifuge at 280 × g for 1 minute.

6.

Vortex the Standard QDNA plate at 1450 rpm for 1 minute.

7.

Centrifuge at 280 × g for 1 minute.

8.

Place the plates on robot bed according to the robot bed map. Remove plate seals.

9.

Transfer PicoGreen/1X TE dilution to half reservoir A and place it on the robot bed.

10.

Deselect the Use Barcodes checkbox.

11.

Select Run.

12.

When the process completes, select OK.

13.

When the robot finishes, immediately seal all plates.

14.

Store DNA and Standard DNA plates at 2° to 8°C or -25°C to -15°C.

15.

Centrifuge Sample QDNA plate and Standard QDNA plate to 280 × g for 1 minute.

This step compares the Sample QDNA plate data to the standard curve to obtain the concentration of sample DNA. For best performance, use a minimum concentration of 50 ng/µl.

1.

Turn on the spectrofluorometer.

2.

Start the SoftMax Pro application.

3.

Load the Illumina QDNA.ppr file from the installation CD.

4.

Select Protocols

5.

Select GTS_QDNA.

6.

Load the Standard QDNA plate into the spectrofluorometer tray with well A1 in the upper left corner.

7.

Select Illumina QDNA

8.

Select SQDNA_STD.

9.

Select Read.

10.

When the spectrofluorometer is finished reading the data, remove the plate from the tray.

11.

Select Standard Curve to view the standard curve graph.

12.

Review generated data and perform one of the following options:

•

Accept the data and continue to the next step.

•

Repeat the Create Standard and Sample QDNA Plates process and regenerate the standard curve.

13.

Load the first Sample QDNA plate in the spectrofluorometer tray with well A1 in the upper left corner.

14.

Select SQDNA, and then select Read.

15.

When the spectrofluorometer is finished reading the data, remove the plate from the tray.

16.

Repeat steps 13–15 to quantify all Sample QDNA plates.

17.

When all plates have been read, select Save to save the output data file (*.pda).

18.

From File, select Import/Export.

19.

Select Export and export the file as a TXT file.

The TXT file can be viewed in Microsoft Excel for data analysis.