Baseline Problems for OLIGO PRO II

Hello everyone,

My team is currently seeing horrible baselines for all 96 wells of our PCR plates that we run on our two Agilent Oligo Pro II. Normally, we see this issue when the temperature in our lab gets above 72-74 degrees F. However, we have since dropped the temperature of the room to 68.6 degrees. The buffers and conditioning gels have all been changed. The CAC box has been changed and the wall plug has been changed onto another wall socket position. Both machines also have separate power sources. My team and I are completely unsure about how to solve the problem. For context, I have added pictures of the baseline fails below.

  • Hi EYO,

    Thank you for sharing the details. I am sorry to hear that you are observing this issue. Based on the description shared, below are possible reasons that may contribute to baseline related issues:

    1. The gel may be contaminated with particulates. Replace the gel bottle, conditioning solution bottle, and buffer plate with new plastic ware. Make new gel. Flush the lines with 0.5N NaOH followed by DI water to ensure lines are clean.
    2. The sample may have become degraded or contaminated. Prepare a new sample aliquot.
    3. There are possible bubbles in the sample wells or capillaries.
      1. Centrifuge the sample plate to ensure there are no bubbles in the sample wells.
      2. Inspect the lines from the Gel and Conditioning Solutions bottles to the pump head for bubbles. Check the fittings and tighten if necessary. Prime the fluid lines to remove any bubbles.
    4. The Oligo Pro II computer has something running in the background using up CPU memory interfering with the data collection of the software. Turn off all updates, screensavers, and sleep-mode.
    5. There is a loose connection to the HUB or USB. Check HUB and USB connections on the Oligo Pro II instrument and CPU. Verify that connections are good.

    If above general recommendations do not resolve the baseline issue, please share the zipped data files as that will show details of the run such as separation parameters, alignment window and actual raw data that are not present in the PDF files. To generate the zipped data file, open the data file in Oligo Pro II Data Analysis software and go to Help>Zip Opened Data file. All the required raw data files will be saved in a zip file in the location of the original data. You will need to do this for the second data file as well. Please send in file for each instrument to In your email to us, please kindly share the serial number for each instrument. Thank you.

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