Qiaxcel handling

Author:

Vinay K L (Originally compiled by Samriddha Ghosh and Saniya Patel in 2018)

Copyright:

None

Date:

07/10/2022

Purpose

To assess the fragment profile of NGS libraries

Before run

  1. Keep the gel cartridge, buffer and tray out for at least 30 min before run. NOTE: The cartridge should always be in upright position.

  2. First switch on the laptop and then the instrument. Open the software.

  3. Check pressure on the instrument. Pressure through out should be more than 30.

  4. If not adjust the pressure with nitrogen cylinder valve and regulator for the inflow. NOTE: First the valve should be open, then adjust the regulator.

  5. Add 6ml QX wash buffer and 2ml Mineral oil to W1 and WP slot of the buffer tray

  6. Add 16ml of separation buffer and 4ml of Mineral oil to Buffer slot of the buffer tray

  7. Add 15 ul of alignment marker compatible with size marker (check for compatibility chart) in a 12-strip tube and place it in the Marker1 position in the buffer tray.

  8. Dilute samples to ~ 10ng/ul and add to another 12 strip tube / plate (for 95 samples)

  9. Dilute size marker to 5, 10 or 20ng/ul based on method. Add this to a empty tube in the samples strip tube or plate.

    NOTE: Size marker 50bp - 1.5kb is only compatible with fast kit/ screening kit. Do not run this with High Res kit.

  10. Insert the cartridge and smart key (plastic node on back). Click on “Latch” under “process” in the software for the instrument to attach the cartridge.

  11. Click on “load position” and open the lid to place the buffer tray, close the lid and then click on “park position”.

  12. Place sample tubes/plate to sample tray.

  13. Go to “Service” > “Maintenance” > “Purge” click on “short purge”, once it is over go for “long purge”.

Software settings

  1. “Process profile” > “process profile” - choose “default highness V 2” for High Resolution kit. Fast profile for screening kit.

  2. “Run parameters” - choose method (OM500 OM800 etc based on fragment size). Right click on size marker position (eg. A1) to define the position.

  3. “Analysis” > check in the box for “smear analysis profile” (only for smear profile ex. library prep).

  4. “Marker” > “marker selection” - check box for “run marker side by side with sample”. Choose appropriate size marker and alignment marker that is being used.

  5. “Sample selection” - enter plate name.

  6. “Sample info” - add sample names.

  7. “Run check” - check box if the 3 criteria are fulfilled. NOTE: If any parameter is not compatible it will show up in yellow, readjust the settings.

  8. Check pressure once more. (preferably stable at ~35).

  9. Start the run.

Post run

  1. After a successful run, select all sample (ctrl + A), go to “Analysis” tab.(on your right side) - Do a analysis with “no marker” - This will align samples with capillary migration.

  2. Do analysis again with the marker table.

  3. Band size and peak height should be available for each sample.

  4. Save report.

Pre-shutting down processes

  1. Open the lid and remove samples and discard them, close the lid.

  2. Click on “load position” to take the buffer tray out. Click on park position after closing the lid.

  3. Keep the buffer tray and alignment marker separately covered with foil in 4 degrees.

  4. Click on “unlatch” and remove the smart key and cartridge. Keep it upright in 4 degrees.

  5. Log out and exit the software.

  6. Switch of the instrument.

  7. close the nitrogen cylinder.

  8. Have a cup of strong coffee.