Planning on analysing microbiome from skin biopsies using QIAGEN Microbiome kit. Can't seem to find the best way to homogenise/lyse samples before proceeding with the manufacturer's instructions.
Any suggestions?
1. Select an appropriate homogenization/lysis method: There are several methods available for homogenizing/lysing skin biopsies, including mechanical disruption (e.g., bead-beating, sonication), chemical lysis (e.g., detergents), and enzymatic lysis. The choice of method depends on the sample type, amount, and quality, as well as the downstream application.
2. Cut the biopsy into small pieces: Use a clean, sharp scalpel to cut the biopsy into small pieces (approximately 1-2 mm). This will help to increase the surface area and facilitate the homogenization/lysis step.
3. Determine the optimal volume of lysis buffer: The amount of lysis buffer required for efficient homogenization/lysis depends on the size and number of the biopsies, as well as the lysis method. It is recommended to use at least 500 µl of lysis buffer per biopsy.
4. Add lysis buffer: Add the appropriate volume of lysis buffer to the biopsy sample in a sterile tube. If using a mechanical method (such as bead-beating or sonication), add a suitable amount of beads to the tube as well.
5. Homogenize/Lyse the sample: Homogenize/Lyse the sample using your chosen method. The duration and intensity of the homogenization/lysis step depends on the method used, and should be optimized for each specific sample.
6. Centrifuge and collect the supernatant: Centrifuge the homogenized/lysed sample at a suitable speed and duration to pellet any debris. Collect the supernatant, which should contain the microbial DNA.
7. Proceed with the manufacturer's instructions: Follow the manufacturer's instructions for DNA extraction, using the collected supernatant as the starting material.
It is recommended to use sterile tools and work in a clean, sterile environment to avoid contamination during the homogenization/lysis step.
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