Best Practices

Best Practices

Prevent PCR Product Contamination

  • Make sure that the lab is set up appropriately to reduce the risk of PCR product contamination. 

Avoid Cross-Contamination

  • Open only one adapter at a time.
  • Using aerosol-resistant pipette tips reduces the risk of nucleic acid carry-over and sample-to-sample cross-contamination. If aerosol-resistant tips are not available, ensure careful pipetting to avoid spillage and contamination.
  • Always use fresh pipette tips between samples and between dispensing index primers, unless specified otherwise.
  • Mix samples using the methods specified in the protocol.
  • Clean pipettes and change gloves between handling different adapter stocks.
  • Clean work surfaces thoroughly before and after the procedure.

Temperature Considerations

  • Keep libraries at temperatures ≤ 37°C, except where specifically noted in a protocol.
  • Place reagents on ice after thawing at room temperature.
  • When processing 48 samples manually, Illumina recommends processing the plate on a bed of ice whenever possible, especially during enzymatic steps (when using the A-Tailing Mix and Ligation Mix). A large number of samples processed at room temperature may result in uneven catalytic activity, which can lead to reduced quality of the end product.
  • Avoid elevated temperatures, particularly in the steps preceding the adapter ligation.
  • Temperature is less of an issue after the adapters have been ligated onto the ends of the ds cDNA.

Handling Liquids

Good liquid handling measures are essential, particularly when quantifying libraries or diluting concentrated libraries for making clusters.

  • Small differences in volumes (±0.5 µl) can sometimes give rise to very large differences in cluster numbers (~100,000).
  • Small volume pipetting can be a source of potential error in protocols that require generation of standard curves, such as PicoGreen assays, or those that require small but precise volumes, such as the Agilent Bioanalyzer.
  • If small volumes are unavoidable, then due diligence should be taken to ensure that pipettes are correctly calibrated.
  • Make sure that pipettes are not used at the volume extremes of their performance specifications.
  • When adapting this protocol for automation or robots, process >16 samples to minimize reagent loss due to dead volume.

Handling Master Mix Reagents

  • Minimize freeze-thaw cycles. If you do not intend to consume the reagents in one use, dispense the reagent into aliquots after the initial thaw and refreeze the aliquots in order to avoid excessive freeze-thaw cycles. However, if you aliquot, you may not have enough reagents for the full number of reactions over multiple uses.
  • Add reagents in the order indicated and avoid making master mixes containing the in-line controls.
  • Take care while adding ATL (A-Tailing Mix) and LIG (Ligation Mix) due to the viscosity of the reagents.
  • Centrifuge the master mix reagents to 600 × g for 5 seconds before use.

Handling Magnetic Beads

Follow appropriate handling methods when working with AMPure XP:

  • Prior to use, allow the beads to come to room temperature.
  • Do not reuse beads. Always add fresh beads when performing the procedures.
  • Immediately prior to use, vortex the beads until they are well dispersed. The color of the liquid should appear homogeneous.
  • After adding the beads to the reaction, seal the plate and shake the plate on a microplate shaker at 1800 rpm for 2 minutes. Repeat, if necessary, until the color of the mixture appears homogeneous after mixing.
  • Take care to minimize bead loss which can impact final yields.
  • Change the tips for each sample.
  • Let the mixed samples incubate at room temperature for the full duration specified in the protocol to ensure maximum recovery.
  • When aspirating the cleared solution from the reaction plate and wash step, it is important to keep the plate on the magnetic stand and to not disturb the separated magnetic beads. Aspirate slowly to prevent the beads from sliding down the sides of the wells and into the pipette tips.
  • To prevent the carryover of beads after elution, approximately 2.5 μl of supernatant are left when the eluates are removed from the bead pellet.
  • Always prepare fresh 80% ethanol, as required in the protocol. Ethanol can absorb water from the air impacting your results.
  • Be sure to remove all of the ethanol from the bottom of the wells, as it may contain residual contaminants. Remaining ethanol can be removed with a 20 μl pipette.
  • Keep the reaction plate on the magnetic stand and let it air-dry at room temperature to prevent potential bead loss due to electrostatic forces.
  • Allow at least 5 minutes of drying time on the magnetic stand at room temperature for complete evaporation. Residual ethanol can impact the performance of subsequent reactions.
  • Do not exceed the recommended drying time as overdrying samples can negatively impact sample recovery and over drying the beads can impact final yields .
  • Resuspend the dried pellets by shaking.
  • When removing and discarding supernatant from the wells, use a single channel or multichannel pipette and take care not to disturb the beads.
  • To maximize sample recovery during elution, incubate the DNA/bead mix for 2 minutes at room temperature before placing the samples onto the magnet.


  • Review the programming instructions for your thermal cycler user guide to ensure that it is programmed appropriately using the heated lid function.
  • Calibrate the microplate shaker with a stroboscope.