# Size selection and clean up considerations for TruSeq DNA PCR Free library preparation

**Can the clean-up step after fragmentation be omitted?**

The clean-up step after fragmentation has been introduced to improve the overall sample success and final yield of the TruSeq PCR-Free library preparation. It is intended to remove impurities that may be present in the input DNA sample. This is routinely performed internally and has been found to improve sample success rate, yield and quality. It is not recommended to skip this clean up step.

**Do purification beads need to be purchased separately for the size selection and clean-up steps?**

No. Each TruSeq DNA PCR-Free kit is supplied with sufficient Sample Purification Beads (SPB) to complete all size selection and clean-up steps in the protocol.

**Can gel electrophoresis be used for size selection in the TruSeq DNA PCR-Free protocol?**

The bead-based size selection step offers several advantages to size selection by gel electrophoresis including speed and sensitivity to sample retention. This should be preferentially used with the PCR-Free kit. The PCR-Free protocol has not been tested using gel-based size selection and the yield may be lower due to increased sample loss.

**What is the recommended drying time for Sample Preparation Beads in the PCR-Free protocol?**

The recommended drying time for the Sample Preparation Beads has been reduced to five to eight minutes depending on the step. Illumina has found that the reduced drying time helps to make sure the beads are dry while minimizing over-drying of the SPB. **Note**: shorter or longer drying times may be required depending on environmental variables and the amount of ethanol remaining in the well. It is important to take care not to over-dry beads as this can impact sample recovery.

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #2777), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002777%20-%20Library%20Preparation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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