Before interpreting samples, confirm that the ladder separated clearly and that positive and negative controls behaved as expected. A weak ladder or contaminated control changes the meaning of every sample lane.
2. Review band quality
Look at product size, band sharpness, background, smearing, and extra bands. A single clean band near the expected size supports proceeding. Multiple bands or smearing may require optimization or cleanup depending on the downstream use.
3. Decide whether cleanup is enough
Cleanup may help remove primers, salts, enzymes, or small fragments, but it will not fix wrong product size or a fundamentally non-specific amplification.
4. Re-measure after cleanup
If the sample will be used for ligation, sequencing, or qPCR standards, re-check concentration after cleanup. Recovery is not always predictable.
5. Record the decision
Write down whether the sample was used directly, cleaned up, excised from gel, repeated, or discarded. This makes later troubleshooting easier if the downstream step fails.
Practical checklist
- Ladder separated correctly.
- Expected band size confirmed.
- Controls behaved correctly.
- Cleanup purpose documented.
- Post-cleanup concentration checked when needed.